diff --git a/Readme.txt b/Readme.txt new file mode 100644 index 0000000..b3606e0 --- /dev/null +++ b/Readme.txt @@ -0,0 +1,27 @@ +Release notes for v2.5 of Argo Based Dynamic Workflow Generator +============================================================== + +Features: +1. Generation of templates and workflow steps for multiple steps in a WGS and WES Pipeline +2. Any template file and Any workflow-steps-file can be provided in the configuration file +3. Support extended to implement scatter-gather from bwa-mem through mark-duplicates for a single sample (upto 4 lanes) +4. Generation of templates from bwa-mem through ApplyBQSR provided +5. Upto 13 intervals supported for BQSR and ApplyBQSR +6. Additional validation of argo configuration file added + +Steps to compile: +Run the ant build.xml cleanall, build, jar +This creates a jar ArgoDynamicWorkflowGenerator.jar +Note: Make sure that the referenced libs commons-io-2.6.jar is on the classpath + +Steps to run: +1) java -cp lib:commons-io-2.6.jar:: Jar-file-from-previous-step configfilename +2) All the template files and configuration files must be on the class path +c) The output file name is .workflow.yaml + +Validate the yaml: +1) Install Argo locally +2) Run argo lint +3) If access to GKE cluster is available, argo submit + + \ No newline at end of file diff --git a/argoworkflow.config.workflow.yaml b/argoworkflow.config.workflow.yaml new file mode 100644 index 0000000..3a3afb2 --- /dev/null +++ b/argoworkflow.config.workflow.yaml @@ -0,0 +1,8250 @@ +####################################################################### +apiVersion: argoproj.io/v2.4.3 +kind: Workflow +metadata: + generateName: argo-dynamically-generated-workflow-hardcodedartifacts +spec: + entrypoint: argo-dynamically-generated-workflow-hardcodedartifacts + templates: +#####################BWA MEM Invoked Template########################## +### The order of variables in this file may not be changed ############ + - name: bwa-mem-001-1 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: gender + artifacts: + - name: fastq1 + path: /tmp/fastq1.fq + - name: fastq2 + path: /tmp/fastq2.fq + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fai + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [sh, -c] + args: [" + cd /tmp; + /usr/gitc/bwa mem -v 3 -t 31 -M + reference.fasta fastq1.fq fastq2.fq | + /usr/local/bin/samtools view -b -S -h - -o /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam ; + /usr/local/bin/samtools sort /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam > /tmp/sortedalignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam ; + /usr/local/bin/samtools index -b /tmp/sortedalignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam /tmp/sortedalignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory : 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-1 + globalName: global-sampleid-001-1 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-1 + globalName: global-laneid-001-1 + valueFrom: + path: /tmp/laneid + - name: gender + globalName: global-gender + valueFrom: + path: /tmp/gender + artifacts: + - name: bwamem-alignedreads-bam-001-1 + globalName: global-bwamemalignedreads-bam-001-1 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bwamem-alignedreads-bai-001-1 + globalName: global-bwamem-alignedreads-bai-001-1 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +#####################BWA MEM Invoked Template########################## +### The order of variables in this file may not be changed ############ + - name: bwa-mem-001-2 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: gender + artifacts: + - name: fastq1 + path: /tmp/fastq1.fq + - name: fastq2 + path: /tmp/fastq2.fq + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fai + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [sh, -c] + args: [" + cd /tmp; + /usr/gitc/bwa mem -v 3 -t 31 -M + reference.fasta fastq1.fq fastq2.fq | + /usr/local/bin/samtools view -b -S -h - -o /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam ; + /usr/local/bin/samtools sort /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam > /tmp/sortedalignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam ; + /usr/local/bin/samtools index -b /tmp/sortedalignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam /tmp/sortedalignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory : 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-2 + globalName: global-sampleid-001-2 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-2 + globalName: global-laneid-001-2 + valueFrom: + path: /tmp/laneid + - name: gender + globalName: global-gender + valueFrom: + path: /tmp/gender + artifacts: + - name: bwamem-alignedreads-bam-001-2 + globalName: global-bwamemalignedreads-bam-001-2 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bwamem-alignedreads-bai-001-2 + globalName: global-bwamem-alignedreads-bai-001-2 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +#####################BWA MEM Invoked Template########################## +### The order of variables in this file may not be changed ############ + - name: bwa-mem-001-3 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: gender + artifacts: + - name: fastq1 + path: /tmp/fastq1.fq + - name: fastq2 + path: /tmp/fastq2.fq + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fai + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [sh, -c] + args: [" + cd /tmp; + /usr/gitc/bwa mem -v 3 -t 31 -M + reference.fasta fastq1.fq fastq2.fq | + /usr/local/bin/samtools view -b -S -h - -o /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam ; + /usr/local/bin/samtools sort /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam > /tmp/sortedalignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam ; + /usr/local/bin/samtools index -b /tmp/sortedalignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam /tmp/sortedalignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory : 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-3 + globalName: global-sampleid-001-3 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-3 + globalName: global-laneid-001-3 + valueFrom: + path: /tmp/laneid + - name: gender + globalName: global-gender + valueFrom: + path: /tmp/gender + artifacts: + - name: bwamem-alignedreads-bam-001-3 + globalName: global-bwamemalignedreads-bam-001-3 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bwamem-alignedreads-bai-001-3 + globalName: global-bwamem-alignedreads-bai-001-3 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +#####################BWA MEM Invoked Template########################## +### The order of variables in this file may not be changed ############ + - name: bwa-mem-001-4 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: gender + artifacts: + - name: fastq1 + path: /tmp/fastq1.fq + - name: fastq2 + path: /tmp/fastq2.fq + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fai + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [sh, -c] + args: [" + cd /tmp; + /usr/gitc/bwa mem -v 3 -t 31 -M + reference.fasta fastq1.fq fastq2.fq | + /usr/local/bin/samtools view -b -S -h - -o /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam ; + /usr/local/bin/samtools sort /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam > /tmp/sortedalignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam ; + /usr/local/bin/samtools index -b /tmp/sortedalignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam /tmp/sortedalignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory : 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-4 + globalName: global-sampleid-001-4 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-4 + globalName: global-laneid-001-4 + valueFrom: + path: /tmp/laneid + - name: gender + globalName: global-gender + valueFrom: + path: /tmp/gender + artifacts: + - name: bwamem-alignedreads-bam-001-4 + globalName: global-bwamemalignedreads-bam-001-4 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bwamem-alignedreads-bai-001-4 + globalName: global-bwamem-alignedreads-bai-001-4 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - name: sort-by-queryname-001-1 + inputs: + parameters: + - name: sampleid + - name: laneid + artifacts: + - name: bwamem-alignedreads-bam-001-1 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + - name: bwamem-alignedreads-bai-001-1 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + /usr/bin/java -Xms1g -Xmx4g -jar /usr/gitc/picard.jar SortSam + INPUT=alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam OUTPUT=/tmp/querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + SORT_ORDER=\"queryname\" CREATE_MD5_FILE=true CREATE_INDEX=true TMP_DIR=`pwd`/tmp 2>/tmp/querynamesort.log;"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-1 + globalName: global-sampleid-001-1 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-1 + globalName: global-laneid-001-1 + valueFrom: + path: /tmp/laneid + artifacts: + - name: querynamesort-logfile-001-1 + globalName: global-querynamesort-logfile-001-1 + path: /tmp/querynamesort.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.querynamesort.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: querynamesort-alignedreads-bam-001-1 + globalName: global-querynamesort-alignedreads-bam-001-1 + path: /tmp/querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: querynamesort-alignedreads-bai-001-1 + globalName: global-querynamesort-alignedreads-bai-001-1 + path: /tmp/querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - name: sort-by-queryname-001-2 + inputs: + parameters: + - name: sampleid + - name: laneid + artifacts: + - name: bwamem-alignedreads-bam-001-2 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + - name: bwamem-alignedreads-bai-001-2 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + /usr/bin/java -Xms1g -Xmx4g -jar /usr/gitc/picard.jar SortSam + INPUT=alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam OUTPUT=/tmp/querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + SORT_ORDER=\"queryname\" CREATE_MD5_FILE=true CREATE_INDEX=true TMP_DIR=`pwd`/tmp 2>/tmp/querynamesort.log;"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-2 + globalName: global-sampleid-001-2 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-2 + globalName: global-laneid-001-2 + valueFrom: + path: /tmp/laneid + artifacts: + - name: querynamesort-logfile-001-2 + globalName: global-querynamesort-logfile-001-2 + path: /tmp/querynamesort.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.querynamesort.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: querynamesort-alignedreads-bam-001-2 + globalName: global-querynamesort-alignedreads-bam-001-2 + path: /tmp/querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: querynamesort-alignedreads-bai-001-2 + globalName: global-querynamesort-alignedreads-bai-001-2 + path: /tmp/querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - name: sort-by-queryname-001-3 + inputs: + parameters: + - name: sampleid + - name: laneid + artifacts: + - name: bwamem-alignedreads-bam-001-3 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + - name: bwamem-alignedreads-bai-001-3 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + /usr/bin/java -Xms1g -Xmx4g -jar /usr/gitc/picard.jar SortSam + INPUT=alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam OUTPUT=/tmp/querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + SORT_ORDER=\"queryname\" CREATE_MD5_FILE=true CREATE_INDEX=true TMP_DIR=`pwd`/tmp 2>/tmp/querynamesort.log;"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-3 + globalName: global-sampleid-001-3 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-3 + globalName: global-laneid-001-3 + valueFrom: + path: /tmp/laneid + artifacts: + - name: querynamesort-logfile-001-3 + globalName: global-querynamesort-logfile-001-3 + path: /tmp/querynamesort.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.querynamesort.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: querynamesort-alignedreads-bam-001-3 + globalName: global-querynamesort-alignedreads-bam-001-3 + path: /tmp/querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: querynamesort-alignedreads-bai-001-3 + globalName: global-querynamesort-alignedreads-bai-001-3 + path: /tmp/querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - name: sort-by-queryname-001-4 + inputs: + parameters: + - name: sampleid + - name: laneid + artifacts: + - name: bwamem-alignedreads-bam-001-4 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + - name: bwamem-alignedreads-bai-001-4 + path: /tmp/alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + /usr/bin/java -Xms1g -Xmx4g -jar /usr/gitc/picard.jar SortSam + INPUT=alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam OUTPUT=/tmp/querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + SORT_ORDER=\"queryname\" CREATE_MD5_FILE=true CREATE_INDEX=true TMP_DIR=`pwd`/tmp 2>/tmp/querynamesort.log;"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-4 + globalName: global-sampleid-001-4 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-4 + globalName: global-laneid-001-4 + valueFrom: + path: /tmp/laneid + artifacts: + - name: querynamesort-logfile-001-4 + globalName: global-querynamesort-logfile-001-4 + path: /tmp/querynamesort.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.querynamesort.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: querynamesort-alignedreads-bam-001-4 + globalName: global-querynamesort-alignedreads-bam-001-4 + path: /tmp/querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: querynamesort-alignedreads-bai-001-4 + globalName: global-querynamesort-alignedreads-bai-001-4 + path: /tmp/querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - name: mark-duplicates-001-1 + inputs: + parameters: + - name: sampleid + - name: laneid + artifacts: + - name: querynamesort-alignedreads-bam-001-1 + path: /tmp/querynamesorted.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + - name: querynamesort-alignedreads-bai-001-1 + path: /tmp/querynamesorted.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/bin/java -Xms2g -Xmx4g -jar /usr/gitc/picard.jar MarkDuplicates + I=querynamesorted.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + O=/tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + M=/tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.metrics VALIDATION_STRINGENCY=SILENT + ASSUME_SORTED=false + REMOVE_DUPLICATES=false + CREATE_INDEX=false CREATE_MD5_FILE=true + OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=`pwd`/tmp 2>/tmp/markduplicates.log;"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-1 + globalName: global-sampleid-001-1 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-1 + globalName: global-laneid-001-1 + valueFrom: + path: /tmp/laneid + artifacts: + - name: markduplicates-logfile-001-1 + globalName: global-markduplicates-logfile-001-1 + path: /tmp/markduplicates.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: markduplicates.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.markduplicates.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: markduplicates-bam-001-1 + globalName: global-markduplicates-dedup-bam-001-1 + path: /tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: markduplicates-metrics-001-1 + globalName: global-markduplicates-metrics-001-1 + path: /tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.metrics + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.metrics + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - name: mark-duplicates-001-2 + inputs: + parameters: + - name: sampleid + - name: laneid + artifacts: + - name: querynamesort-alignedreads-bam-001-2 + path: /tmp/querynamesorted.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + - name: querynamesort-alignedreads-bai-001-2 + path: /tmp/querynamesorted.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/bin/java -Xms2g -Xmx4g -jar /usr/gitc/picard.jar MarkDuplicates + I=querynamesorted.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + O=/tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + M=/tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.metrics VALIDATION_STRINGENCY=SILENT + ASSUME_SORTED=false + REMOVE_DUPLICATES=false + CREATE_INDEX=false CREATE_MD5_FILE=true + OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=`pwd`/tmp 2>/tmp/markduplicates.log;"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-2 + globalName: global-sampleid-001-2 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-2 + globalName: global-laneid-001-2 + valueFrom: + path: /tmp/laneid + artifacts: + - name: markduplicates-logfile-001-2 + globalName: global-markduplicates-logfile-001-2 + path: /tmp/markduplicates.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: markduplicates.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.markduplicates.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: markduplicates-bam-001-2 + globalName: global-markduplicates-dedup-bam-001-2 + path: /tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: markduplicates-metrics-001-2 + globalName: global-markduplicates-metrics-001-2 + path: /tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.metrics + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.metrics + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - name: mark-duplicates-001-3 + inputs: + parameters: + - name: sampleid + - name: laneid + artifacts: + - name: querynamesort-alignedreads-bam-001-3 + path: /tmp/querynamesorted.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + - name: querynamesort-alignedreads-bai-001-3 + path: /tmp/querynamesorted.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/bin/java -Xms2g -Xmx4g -jar /usr/gitc/picard.jar MarkDuplicates + I=querynamesorted.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + O=/tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + M=/tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.metrics VALIDATION_STRINGENCY=SILENT + ASSUME_SORTED=false + REMOVE_DUPLICATES=false + CREATE_INDEX=false CREATE_MD5_FILE=true + OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=`pwd`/tmp 2>/tmp/markduplicates.log;"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-3 + globalName: global-sampleid-001-3 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-3 + globalName: global-laneid-001-3 + valueFrom: + path: /tmp/laneid + artifacts: + - name: markduplicates-logfile-001-3 + globalName: global-markduplicates-logfile-001-3 + path: /tmp/markduplicates.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: markduplicates.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.markduplicates.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: markduplicates-bam-001-3 + globalName: global-markduplicates-dedup-bam-001-3 + path: /tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: markduplicates-metrics-001-3 + globalName: global-markduplicates-metrics-001-3 + path: /tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.metrics + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.metrics + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - name: mark-duplicates-001-4 + inputs: + parameters: + - name: sampleid + - name: laneid + artifacts: + - name: querynamesort-alignedreads-bam-001-4 + path: /tmp/querynamesorted.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + - name: querynamesort-alignedreads-bai-001-4 + path: /tmp/querynamesorted.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/bin/java -Xms2g -Xmx4g -jar /usr/gitc/picard.jar MarkDuplicates + I=querynamesorted.alignedreads.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + O=/tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + M=/tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.metrics VALIDATION_STRINGENCY=SILENT + ASSUME_SORTED=false + REMOVE_DUPLICATES=false + CREATE_INDEX=false CREATE_MD5_FILE=true + OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=`pwd`/tmp 2>/tmp/markduplicates.log;"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-4 + globalName: global-sampleid-001-4 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-4 + globalName: global-laneid-001-4 + valueFrom: + path: /tmp/laneid + artifacts: + - name: markduplicates-logfile-001-4 + globalName: global-markduplicates-logfile-001-4 + path: /tmp/markduplicates.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: markduplicates.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.markduplicates.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: markduplicates-bam-001-4 + globalName: global-markduplicates-dedup-bam-001-4 + path: /tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: markduplicates-metrics-001-4 + globalName: global-markduplicates-metrics-001-4 + path: /tmp/dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.metrics + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: dedup.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.metrics + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +## Merge BAMs ######################################################### +####################################################################### + - name: merge-bams-001-1 + inputs: + parameters: + - name: sampleid + - name: previousstepname + artifacts: + - name: markduplicates-bam-001-1 + path: /tmp/markduplicates-bam-001-1.bam + - name: markduplicates-bam-001-2 + path: /tmp/markduplicates-bam-001-2.bam + - name: markduplicates-bam-001-3 + path: /tmp/markduplicates-bam-001-3.bam + - name: markduplicates-bam-001-4 + path: /tmp/markduplicates-bam-001-4.bam + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + /usr/bin/java -Xms2g -Xmx4g -jar /usr/gitc/picard.jar MergeSamFiles INPUT=/tmp/markduplicates-bam-001-1.bam INPUT=/tmp/markduplicates-bam-001-2.bam INPUT=/tmp/markduplicates-bam-001-3.bam INPUT=/tmp/markduplicates-bam-001-4.bam + OUTPUT=/tmp/mergebams.{{inputs.parameters.sampleid}}.{{inputs.parameters.previousstepname}}.bam + CREATE_MD5_FILE=true TMP_DIR=`pwd`/tmp CREATE_INDEX=false >/tmp/mergebams.{{inputs.parameters.sampleid}}.{{inputs.parameters.previousstepname}}.log;"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-1 + globalName: global-sampleid-001-1 + valueFrom: + path: /tmp/sampleid + artifacts: + - name: mergebams-logfile-001-1 + globalName: global-mergebams-markduplicates-bam-001-1 + path: /tmp/mergebams.{{inputs.parameters.sampleid}}.{{inputs.parameters.previousstepname}}.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: mergebams.{{inputs.parameters.sampleid}}.{{inputs.parameters.previousstepname}}.gatk.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: mergebams-bam-001-1 + globalName: global-mergebams-markduplicates-bam-001-1 + path: /tmp/mergebams.{{inputs.parameters.sampleid}}.{{inputs.parameters.previousstepname}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: mergebams.{{inputs.parameters.sampleid}}.{{inputs.parameters.previousstepname}}.bam + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - name: sort-by-coordinate-001-1 + inputs: + parameters: + - name: sampleid + - name: laneid + artifacts: + - name: mergebams-bam-001-1 + path: /tmp/mergebams.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + /usr/bin/java -Xms1g -Xmx4g -jar /usr/gitc/picard.jar SortSam + INPUT=mergebams.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam OUTPUT=/tmp/coordinatesort.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + SORT_ORDER=\"coordinate\" CREATE_MD5_FILE=true CREATE_INDEX=true TMP_DIR=`pwd`/tmp 2>/tmp/coordinatesort.log;"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-1 + globalName: global-sampleid-001-1 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-1 + globalName: global-laneid-001-1 + valueFrom: + path: /tmp/laneid + artifacts: + - name: coordinatesort-logfile-001-1 + globalName: global-coordinatesort-logfile-001-1 + path: /tmp/coordinatesort.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.coordinatesort.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: coordinatesort-bam-001-1 + globalName: global-coordinatesort-alignedreads-bam-001-1 + path: /tmp/coordinatesort.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: coordinatesort-bai-001-1 + globalName: global-coordinatesort-alignedreads-bai-001-1 + path: /tmp/coordinatesort.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Base Recalibration ############################################### +####################################################################### + - name: base-recalibration-001-Interval1 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: dbsnp + path: /tmp/dbSNP.vcf.gz + - name: dbsnp-tbi + path: /tmp/dbSNP.vcf.gz.tbi + - name: gold-standard-indels-vcf + path: /tmp/gold_standard.indels.vcf + - name: gold-standard-indels-vcf-idx + path: /tmp/gold_standard.indels.vcf.idx + - name: intervalslist + path: /tmp/intervals.interval_list +####################################################################### + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bai; + /usr/bin/java -Xms4G -Xmx6G -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T BaseRecalibrator -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam + -o /tmp/recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + -L intervals.interval_list + -knownSites /tmp/gold_standard.indels.vcf 2>/tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval1 + globalName: global-sampleid-001-Interval1 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-Interval1 + globalName: global-laneid-001-Interval1 + valueFrom: + path: /tmp/laneid + artifacts: + - name: bqsr-logfile-001-Interval1 + globalName: global-bqsr-logfile-001-Interval1 + path: /tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bqsr-recalibration-report-001-Interval1 + globalName: global-bqsr-recalibration-report-001-Interval1 + path: /tmp/bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Apply Base Recalibration ######################################### + - name: apply-bqsr-001-Interval1 + inputs: + parameters: + - name: sampleid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: recalibration-report + path: /tmp/recalibration.table + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bam.bai; + /usr/bin/java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal + -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails + -Xloggc:gc_log.log -Dsamjdk.use_async_io=false + -Xms2g -Xmx4g -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T PrintReads -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam -o /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + --BQSR /tmp/recalibration.table 2>/tmp/applybqsr.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval1 + globalName: global-sampleid-001-Interval1 + valueFrom: + path: /tmp/sampleid + artifacts: + - name: applybqsr-logfile-001-Interval1 + globalName: global-applybqsr-logfile-001-Interval1 + path: /tmp/applybqsr.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: applybqsr-bam-001-Interval1 + globalName: global-applybqsr-bam-001-Interval1 + path: /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Base Recalibration ############################################### +####################################################################### + - name: base-recalibration-001-Interval2 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: dbsnp + path: /tmp/dbSNP.vcf.gz + - name: dbsnp-tbi + path: /tmp/dbSNP.vcf.gz.tbi + - name: gold-standard-indels-vcf + path: /tmp/gold_standard.indels.vcf + - name: gold-standard-indels-vcf-idx + path: /tmp/gold_standard.indels.vcf.idx + - name: intervalslist + path: /tmp/intervals.interval_list +####################################################################### + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bai; + /usr/bin/java -Xms4G -Xmx6G -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T BaseRecalibrator -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam + -o /tmp/recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + -L intervals.interval_list + -knownSites /tmp/gold_standard.indels.vcf 2>/tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval2 + globalName: global-sampleid-001-Interval2 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-Interval2 + globalName: global-laneid-001-Interval2 + valueFrom: + path: /tmp/laneid + artifacts: + - name: bqsr-logfile-001-Interval2 + globalName: global-bqsr-logfile-001-Interval2 + path: /tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bqsr-recalibration-report-001-Interval2 + globalName: global-bqsr-recalibration-report-001-Interval2 + path: /tmp/bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Apply Base Recalibration ######################################### + - name: apply-bqsr-001-Interval2 + inputs: + parameters: + - name: sampleid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: recalibration-report + path: /tmp/recalibration.table + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bam.bai; + /usr/bin/java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal + -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails + -Xloggc:gc_log.log -Dsamjdk.use_async_io=false + -Xms2g -Xmx4g -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T PrintReads -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam -o /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + --BQSR /tmp/recalibration.table 2>/tmp/applybqsr.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval2 + globalName: global-sampleid-001-Interval2 + valueFrom: + path: /tmp/sampleid + artifacts: + - name: applybqsr-logfile-001-Interval2 + globalName: global-applybqsr-logfile-001-Interval2 + path: /tmp/applybqsr.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: applybqsr-bam-001-Interval2 + globalName: global-applybqsr-bam-001-Interval2 + path: /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Base Recalibration ############################################### +####################################################################### + - name: base-recalibration-001-Interval3 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: dbsnp + path: /tmp/dbSNP.vcf.gz + - name: dbsnp-tbi + path: /tmp/dbSNP.vcf.gz.tbi + - name: gold-standard-indels-vcf + path: /tmp/gold_standard.indels.vcf + - name: gold-standard-indels-vcf-idx + path: /tmp/gold_standard.indels.vcf.idx + - name: intervalslist + path: /tmp/intervals.interval_list +####################################################################### + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bai; + /usr/bin/java -Xms4G -Xmx6G -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T BaseRecalibrator -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam + -o /tmp/recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + -L intervals.interval_list + -knownSites /tmp/gold_standard.indels.vcf 2>/tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval3 + globalName: global-sampleid-001-Interval3 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-Interval3 + globalName: global-laneid-001-Interval3 + valueFrom: + path: /tmp/laneid + artifacts: + - name: bqsr-logfile-001-Interval3 + globalName: global-bqsr-logfile-001-Interval3 + path: /tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bqsr-recalibration-report-001-Interval3 + globalName: global-bqsr-recalibration-report-001-Interval3 + path: /tmp/bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Apply Base Recalibration ######################################### + - name: apply-bqsr-001-Interval3 + inputs: + parameters: + - name: sampleid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: recalibration-report + path: /tmp/recalibration.table + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bam.bai; + /usr/bin/java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal + -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails + -Xloggc:gc_log.log -Dsamjdk.use_async_io=false + -Xms2g -Xmx4g -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T PrintReads -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam -o /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + --BQSR /tmp/recalibration.table 2>/tmp/applybqsr.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval3 + globalName: global-sampleid-001-Interval3 + valueFrom: + path: /tmp/sampleid + artifacts: + - name: applybqsr-logfile-001-Interval3 + globalName: global-applybqsr-logfile-001-Interval3 + path: /tmp/applybqsr.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: applybqsr-bam-001-Interval3 + globalName: global-applybqsr-bam-001-Interval3 + path: /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Base Recalibration ############################################### +####################################################################### + - name: base-recalibration-001-Interval4 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: dbsnp + path: /tmp/dbSNP.vcf.gz + - name: dbsnp-tbi + path: /tmp/dbSNP.vcf.gz.tbi + - name: gold-standard-indels-vcf + path: /tmp/gold_standard.indels.vcf + - name: gold-standard-indels-vcf-idx + path: /tmp/gold_standard.indels.vcf.idx + - name: intervalslist + path: /tmp/intervals.interval_list +####################################################################### + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bai; + /usr/bin/java -Xms4G -Xmx6G -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T BaseRecalibrator -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam + -o /tmp/recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + -L intervals.interval_list + -knownSites /tmp/gold_standard.indels.vcf 2>/tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval4 + globalName: global-sampleid-001-Interval4 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-Interval4 + globalName: global-laneid-001-Interval4 + valueFrom: + path: /tmp/laneid + artifacts: + - name: bqsr-logfile-001-Interval4 + globalName: global-bqsr-logfile-001-Interval4 + path: /tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bqsr-recalibration-report-001-Interval4 + globalName: global-bqsr-recalibration-report-001-Interval4 + path: /tmp/bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Apply Base Recalibration ######################################### + - name: apply-bqsr-001-Interval4 + inputs: + parameters: + - name: sampleid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: recalibration-report + path: /tmp/recalibration.table + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bam.bai; + /usr/bin/java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal + -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails + -Xloggc:gc_log.log -Dsamjdk.use_async_io=false + -Xms2g -Xmx4g -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T PrintReads -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam -o /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + --BQSR /tmp/recalibration.table 2>/tmp/applybqsr.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval4 + globalName: global-sampleid-001-Interval4 + valueFrom: + path: /tmp/sampleid + artifacts: + - name: applybqsr-logfile-001-Interval4 + globalName: global-applybqsr-logfile-001-Interval4 + path: /tmp/applybqsr.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: applybqsr-bam-001-Interval4 + globalName: global-applybqsr-bam-001-Interval4 + path: /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Base Recalibration ############################################### +####################################################################### + - name: base-recalibration-001-Interval5 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: dbsnp + path: /tmp/dbSNP.vcf.gz + - name: dbsnp-tbi + path: /tmp/dbSNP.vcf.gz.tbi + - name: gold-standard-indels-vcf + path: /tmp/gold_standard.indels.vcf + - name: gold-standard-indels-vcf-idx + path: /tmp/gold_standard.indels.vcf.idx + - name: intervalslist + path: /tmp/intervals.interval_list +####################################################################### + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bai; + /usr/bin/java -Xms4G -Xmx6G -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T BaseRecalibrator -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam + -o /tmp/recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + -L intervals.interval_list + -knownSites /tmp/gold_standard.indels.vcf 2>/tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval5 + globalName: global-sampleid-001-Interval5 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-Interval5 + globalName: global-laneid-001-Interval5 + valueFrom: + path: /tmp/laneid + artifacts: + - name: bqsr-logfile-001-Interval5 + globalName: global-bqsr-logfile-001-Interval5 + path: /tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bqsr-recalibration-report-001-Interval5 + globalName: global-bqsr-recalibration-report-001-Interval5 + path: /tmp/bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Apply Base Recalibration ######################################### + - name: apply-bqsr-001-Interval5 + inputs: + parameters: + - name: sampleid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: recalibration-report + path: /tmp/recalibration.table + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bam.bai; + /usr/bin/java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal + -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails + -Xloggc:gc_log.log -Dsamjdk.use_async_io=false + -Xms2g -Xmx4g -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T PrintReads -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam -o /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + --BQSR /tmp/recalibration.table 2>/tmp/applybqsr.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval5 + globalName: global-sampleid-001-Interval5 + valueFrom: + path: /tmp/sampleid + artifacts: + - name: applybqsr-logfile-001-Interval5 + globalName: global-applybqsr-logfile-001-Interval5 + path: /tmp/applybqsr.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: applybqsr-bam-001-Interval5 + globalName: global-applybqsr-bam-001-Interval5 + path: /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Base Recalibration ############################################### +####################################################################### + - name: base-recalibration-001-Interval6 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: dbsnp + path: /tmp/dbSNP.vcf.gz + - name: dbsnp-tbi + path: /tmp/dbSNP.vcf.gz.tbi + - name: gold-standard-indels-vcf + path: /tmp/gold_standard.indels.vcf + - name: gold-standard-indels-vcf-idx + path: /tmp/gold_standard.indels.vcf.idx + - name: intervalslist + path: /tmp/intervals.interval_list +####################################################################### + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bai; + /usr/bin/java -Xms4G -Xmx6G -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T BaseRecalibrator -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam + -o /tmp/recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + -L intervals.interval_list + -knownSites /tmp/gold_standard.indels.vcf 2>/tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval6 + globalName: global-sampleid-001-Interval6 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-Interval6 + globalName: global-laneid-001-Interval6 + valueFrom: + path: /tmp/laneid + artifacts: + - name: bqsr-logfile-001-Interval6 + globalName: global-bqsr-logfile-001-Interval6 + path: /tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bqsr-recalibration-report-001-Interval6 + globalName: global-bqsr-recalibration-report-001-Interval6 + path: /tmp/bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Apply Base Recalibration ######################################### + - name: apply-bqsr-001-Interval6 + inputs: + parameters: + - name: sampleid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: recalibration-report + path: /tmp/recalibration.table + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bam.bai; + /usr/bin/java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal + -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails + -Xloggc:gc_log.log -Dsamjdk.use_async_io=false + -Xms2g -Xmx4g -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T PrintReads -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam -o /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + --BQSR /tmp/recalibration.table 2>/tmp/applybqsr.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval6 + globalName: global-sampleid-001-Interval6 + valueFrom: + path: /tmp/sampleid + artifacts: + - name: applybqsr-logfile-001-Interval6 + globalName: global-applybqsr-logfile-001-Interval6 + path: /tmp/applybqsr.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: applybqsr-bam-001-Interval6 + globalName: global-applybqsr-bam-001-Interval6 + path: /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Base Recalibration ############################################### +####################################################################### + - name: base-recalibration-001-Interval7 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: dbsnp + path: /tmp/dbSNP.vcf.gz + - name: dbsnp-tbi + path: /tmp/dbSNP.vcf.gz.tbi + - name: gold-standard-indels-vcf + path: /tmp/gold_standard.indels.vcf + - name: gold-standard-indels-vcf-idx + path: /tmp/gold_standard.indels.vcf.idx + - name: intervalslist + path: /tmp/intervals.interval_list +####################################################################### + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bai; + /usr/bin/java -Xms4G -Xmx6G -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T BaseRecalibrator -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam + -o /tmp/recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + -L intervals.interval_list + -knownSites /tmp/gold_standard.indels.vcf 2>/tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval7 + globalName: global-sampleid-001-Interval7 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-Interval7 + globalName: global-laneid-001-Interval7 + valueFrom: + path: /tmp/laneid + artifacts: + - name: bqsr-logfile-001-Interval7 + globalName: global-bqsr-logfile-001-Interval7 + path: /tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bqsr-recalibration-report-001-Interval7 + globalName: global-bqsr-recalibration-report-001-Interval7 + path: /tmp/bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Apply Base Recalibration ######################################### + - name: apply-bqsr-001-Interval7 + inputs: + parameters: + - name: sampleid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: recalibration-report + path: /tmp/recalibration.table + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bam.bai; + /usr/bin/java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal + -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails + -Xloggc:gc_log.log -Dsamjdk.use_async_io=false + -Xms2g -Xmx4g -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T PrintReads -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam -o /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + --BQSR /tmp/recalibration.table 2>/tmp/applybqsr.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval7 + globalName: global-sampleid-001-Interval7 + valueFrom: + path: /tmp/sampleid + artifacts: + - name: applybqsr-logfile-001-Interval7 + globalName: global-applybqsr-logfile-001-Interval7 + path: /tmp/applybqsr.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: applybqsr-bam-001-Interval7 + globalName: global-applybqsr-bam-001-Interval7 + path: /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Base Recalibration ############################################### +####################################################################### + - name: base-recalibration-001-Interval8 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: dbsnp + path: /tmp/dbSNP.vcf.gz + - name: dbsnp-tbi + path: /tmp/dbSNP.vcf.gz.tbi + - name: gold-standard-indels-vcf + path: /tmp/gold_standard.indels.vcf + - name: gold-standard-indels-vcf-idx + path: /tmp/gold_standard.indels.vcf.idx + - name: intervalslist + path: /tmp/intervals.interval_list +####################################################################### + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bai; + /usr/bin/java -Xms4G -Xmx6G -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T BaseRecalibrator -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam + -o /tmp/recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + -L intervals.interval_list + -knownSites /tmp/gold_standard.indels.vcf 2>/tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval8 + globalName: global-sampleid-001-Interval8 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-Interval8 + globalName: global-laneid-001-Interval8 + valueFrom: + path: /tmp/laneid + artifacts: + - name: bqsr-logfile-001-Interval8 + globalName: global-bqsr-logfile-001-Interval8 + path: /tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bqsr-recalibration-report-001-Interval8 + globalName: global-bqsr-recalibration-report-001-Interval8 + path: /tmp/bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Apply Base Recalibration ######################################### + - name: apply-bqsr-001-Interval8 + inputs: + parameters: + - name: sampleid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: recalibration-report + path: /tmp/recalibration.table + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bam.bai; + /usr/bin/java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal + -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails + -Xloggc:gc_log.log -Dsamjdk.use_async_io=false + -Xms2g -Xmx4g -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T PrintReads -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam -o /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + --BQSR /tmp/recalibration.table 2>/tmp/applybqsr.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval8 + globalName: global-sampleid-001-Interval8 + valueFrom: + path: /tmp/sampleid + artifacts: + - name: applybqsr-logfile-001-Interval8 + globalName: global-applybqsr-logfile-001-Interval8 + path: /tmp/applybqsr.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: applybqsr-bam-001-Interval8 + globalName: global-applybqsr-bam-001-Interval8 + path: /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Base Recalibration ############################################### +####################################################################### + - name: base-recalibration-001-Interval9 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: dbsnp + path: /tmp/dbSNP.vcf.gz + - name: dbsnp-tbi + path: /tmp/dbSNP.vcf.gz.tbi + - name: gold-standard-indels-vcf + path: /tmp/gold_standard.indels.vcf + - name: gold-standard-indels-vcf-idx + path: /tmp/gold_standard.indels.vcf.idx + - name: intervalslist + path: /tmp/intervals.interval_list +####################################################################### + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bai; + /usr/bin/java -Xms4G -Xmx6G -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T BaseRecalibrator -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam + -o /tmp/recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + -L intervals.interval_list + -knownSites /tmp/gold_standard.indels.vcf 2>/tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval9 + globalName: global-sampleid-001-Interval9 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-Interval9 + globalName: global-laneid-001-Interval9 + valueFrom: + path: /tmp/laneid + artifacts: + - name: bqsr-logfile-001-Interval9 + globalName: global-bqsr-logfile-001-Interval9 + path: /tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bqsr-recalibration-report-001-Interval9 + globalName: global-bqsr-recalibration-report-001-Interval9 + path: /tmp/bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Apply Base Recalibration ######################################### + - name: apply-bqsr-001-Interval9 + inputs: + parameters: + - name: sampleid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: recalibration-report + path: /tmp/recalibration.table + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bam.bai; + /usr/bin/java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal + -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails + -Xloggc:gc_log.log -Dsamjdk.use_async_io=false + -Xms2g -Xmx4g -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T PrintReads -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam -o /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + --BQSR /tmp/recalibration.table 2>/tmp/applybqsr.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval9 + globalName: global-sampleid-001-Interval9 + valueFrom: + path: /tmp/sampleid + artifacts: + - name: applybqsr-logfile-001-Interval9 + globalName: global-applybqsr-logfile-001-Interval9 + path: /tmp/applybqsr.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: applybqsr-bam-001-Interval9 + globalName: global-applybqsr-bam-001-Interval9 + path: /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Base Recalibration ############################################### +####################################################################### + - name: base-recalibration-001-Interval10 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: dbsnp + path: /tmp/dbSNP.vcf.gz + - name: dbsnp-tbi + path: /tmp/dbSNP.vcf.gz.tbi + - name: gold-standard-indels-vcf + path: /tmp/gold_standard.indels.vcf + - name: gold-standard-indels-vcf-idx + path: /tmp/gold_standard.indels.vcf.idx + - name: intervalslist + path: /tmp/intervals.interval_list +####################################################################### + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bai; + /usr/bin/java -Xms4G -Xmx6G -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T BaseRecalibrator -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam + -o /tmp/recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + -L intervals.interval_list + -knownSites /tmp/gold_standard.indels.vcf 2>/tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval10 + globalName: global-sampleid-001-Interval10 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-Interval10 + globalName: global-laneid-001-Interval10 + valueFrom: + path: /tmp/laneid + artifacts: + - name: bqsr-logfile-001-Interval10 + globalName: global-bqsr-logfile-001-Interval10 + path: /tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bqsr-recalibration-report-001-Interval10 + globalName: global-bqsr-recalibration-report-001-Interval10 + path: /tmp/bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Apply Base Recalibration ######################################### + - name: apply-bqsr-001-Interval10 + inputs: + parameters: + - name: sampleid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: recalibration-report + path: /tmp/recalibration.table + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bam.bai; + /usr/bin/java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal + -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails + -Xloggc:gc_log.log -Dsamjdk.use_async_io=false + -Xms2g -Xmx4g -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T PrintReads -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam -o /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + --BQSR /tmp/recalibration.table 2>/tmp/applybqsr.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval10 + globalName: global-sampleid-001-Interval10 + valueFrom: + path: /tmp/sampleid + artifacts: + - name: applybqsr-logfile-001-Interval10 + globalName: global-applybqsr-logfile-001-Interval10 + path: /tmp/applybqsr.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: applybqsr-bam-001-Interval10 + globalName: global-applybqsr-bam-001-Interval10 + path: /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Base Recalibration ############################################### +####################################################################### + - name: base-recalibration-001-Interval11 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: dbsnp + path: /tmp/dbSNP.vcf.gz + - name: dbsnp-tbi + path: /tmp/dbSNP.vcf.gz.tbi + - name: gold-standard-indels-vcf + path: /tmp/gold_standard.indels.vcf + - name: gold-standard-indels-vcf-idx + path: /tmp/gold_standard.indels.vcf.idx + - name: intervalslist + path: /tmp/intervals.interval_list +####################################################################### + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bai; + /usr/bin/java -Xms4G -Xmx6G -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T BaseRecalibrator -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam + -o /tmp/recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + -L intervals.interval_list + -knownSites /tmp/gold_standard.indels.vcf 2>/tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval11 + globalName: global-sampleid-001-Interval11 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-Interval11 + globalName: global-laneid-001-Interval11 + valueFrom: + path: /tmp/laneid + artifacts: + - name: bqsr-logfile-001-Interval11 + globalName: global-bqsr-logfile-001-Interval11 + path: /tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bqsr-recalibration-report-001-Interval11 + globalName: global-bqsr-recalibration-report-001-Interval11 + path: /tmp/bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Apply Base Recalibration ######################################### + - name: apply-bqsr-001-Interval11 + inputs: + parameters: + - name: sampleid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: recalibration-report + path: /tmp/recalibration.table + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bam.bai; + /usr/bin/java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal + -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails + -Xloggc:gc_log.log -Dsamjdk.use_async_io=false + -Xms2g -Xmx4g -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T PrintReads -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam -o /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + --BQSR /tmp/recalibration.table 2>/tmp/applybqsr.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval11 + globalName: global-sampleid-001-Interval11 + valueFrom: + path: /tmp/sampleid + artifacts: + - name: applybqsr-logfile-001-Interval11 + globalName: global-applybqsr-logfile-001-Interval11 + path: /tmp/applybqsr.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: applybqsr-bam-001-Interval11 + globalName: global-applybqsr-bam-001-Interval11 + path: /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Base Recalibration ############################################### +####################################################################### + - name: base-recalibration-001-Interval12 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: dbsnp + path: /tmp/dbSNP.vcf.gz + - name: dbsnp-tbi + path: /tmp/dbSNP.vcf.gz.tbi + - name: gold-standard-indels-vcf + path: /tmp/gold_standard.indels.vcf + - name: gold-standard-indels-vcf-idx + path: /tmp/gold_standard.indels.vcf.idx + - name: intervalslist + path: /tmp/intervals.interval_list +####################################################################### + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bai; + /usr/bin/java -Xms4G -Xmx6G -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T BaseRecalibrator -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam + -o /tmp/recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + -L intervals.interval_list + -knownSites /tmp/gold_standard.indels.vcf 2>/tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval12 + globalName: global-sampleid-001-Interval12 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-Interval12 + globalName: global-laneid-001-Interval12 + valueFrom: + path: /tmp/laneid + artifacts: + - name: bqsr-logfile-001-Interval12 + globalName: global-bqsr-logfile-001-Interval12 + path: /tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bqsr-recalibration-report-001-Interval12 + globalName: global-bqsr-recalibration-report-001-Interval12 + path: /tmp/bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Apply Base Recalibration ######################################### + - name: apply-bqsr-001-Interval12 + inputs: + parameters: + - name: sampleid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: recalibration-report + path: /tmp/recalibration.table + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bam.bai; + /usr/bin/java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal + -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails + -Xloggc:gc_log.log -Dsamjdk.use_async_io=false + -Xms2g -Xmx4g -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T PrintReads -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam -o /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + --BQSR /tmp/recalibration.table 2>/tmp/applybqsr.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval12 + globalName: global-sampleid-001-Interval12 + valueFrom: + path: /tmp/sampleid + artifacts: + - name: applybqsr-logfile-001-Interval12 + globalName: global-applybqsr-logfile-001-Interval12 + path: /tmp/applybqsr.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: applybqsr-bam-001-Interval12 + globalName: global-applybqsr-bam-001-Interval12 + path: /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Base Recalibration ############################################### +####################################################################### + - name: base-recalibration-001-Interval13 + inputs: + parameters: + - name: sampleid + - name: laneid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: dbsnp + path: /tmp/dbSNP.vcf.gz + - name: dbsnp-tbi + path: /tmp/dbSNP.vcf.gz.tbi + - name: gold-standard-indels-vcf + path: /tmp/gold_standard.indels.vcf + - name: gold-standard-indels-vcf-idx + path: /tmp/gold_standard.indels.vcf.idx + - name: intervalslist + path: /tmp/intervals.interval_list +####################################################################### + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bai; + /usr/bin/java -Xms4G -Xmx6G -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T BaseRecalibrator -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam + -o /tmp/recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + -L intervals.interval_list + -knownSites /tmp/gold_standard.indels.vcf 2>/tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval13 + globalName: global-sampleid-001-Interval13 + valueFrom: + path: /tmp/sampleid + - name: laneid-001-Interval13 + globalName: global-laneid-001-Interval13 + valueFrom: + path: /tmp/laneid + artifacts: + - name: bqsr-logfile-001-Interval13 + globalName: global-bqsr-logfile-001-Interval13 + path: /tmp/bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bqsr-recalibration-report-001-Interval13 + globalName: global-bqsr-recalibration-report-001-Interval13 + path: /tmp/bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.{{inputs.parameters.sampleid}}.{{inputs.parameters.laneid}}.{{inputs.parameters.intervalnumber}}.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +#### Apply Base Recalibration ######################################### + - name: apply-bqsr-001-Interval13 + inputs: + parameters: + - name: sampleid + - name: intervalnumber + artifacts: + - name: coordinatesort-bam + path: /tmp/coordinatesort.bam + - name: reference-files-sa + path: /tmp/reference.fasta.sa + - name: reference-files-amb + path: /tmp/reference.fasta.amb + - name: reference-files-ann + path: /tmp/reference.fasta.ann + - name: reference-files-bwt + path: /tmp/reference.fasta.bwt + - name: reference-files-dict + path: /tmp/reference.dict + - name: reference-files-pac + path: /tmp/reference.fasta.pac + - name: reference-files-fasta + path: /tmp/reference.fasta + - name: reference-files-fai + path: /tmp/reference.fasta.fai + - name: recalibration-report + path: /tmp/recalibration.table + retryStrategy: + limit: 10 + container: + image: vandhanak/broadcloudgatk36gatk37-cgs:0.2 + command: [bash, -c] + args: [" + cd /tmp; + /usr/local/bin/samtools index -b /tmp/coordinatesort.bam + /tmp/coordinatesort.bam.bai; + /usr/bin/java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal + -XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails + -Xloggc:gc_log.log -Dsamjdk.use_async_io=false + -Xms2g -Xmx4g -jar /usr/gitc/gatk37/GenomeAnalysisTK.jar + -T PrintReads -R /tmp/reference.fasta + -I /tmp/coordinatesort.bam -o /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + --BQSR /tmp/recalibration.table 2>/tmp/applybqsr.log"] + resources: + limits: + memory : 8000Mi + cpu: 10 + requests: + memory: 2000Mi + cpu: 4 + activeDeadlineSeconds: 7200 + outputs: + parameters: + - name: sampleid-001-Interval13 + globalName: global-sampleid-001-Interval13 + valueFrom: + path: /tmp/sampleid + artifacts: + - name: applybqsr-logfile-001-Interval13 + globalName: global-applybqsr-logfile-001-Interval13 + path: /tmp/applybqsr.log + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.log + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: applybqsr-bam-001-Interval13 + globalName: global-applybqsr-bam-001-Interval13 + path: /tmp/applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: applybqsr.{{inputs.parameters.sampleid}}.{{inputs.parameters.intervalnumber}}.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - name: argo-dynamically-generated-workflow-hardcodedartifacts + steps: +####################################################################### +####################################################################### + - - name: bwamem-001-1 + template: bwa-mem-001-1 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + - name: gender + value: "M" + artifacts: + - name: fastq1 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: SP11.fq + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: fastq2 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: SP12.fq + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - - name: bwamem-001-2 + template: bwa-mem-001-2 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "2" + - name: gender + value: "M" + artifacts: + - name: fastq1 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: SP21.fq + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: fastq2 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: SP22.fq + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - - name: bwamem-001-3 + template: bwa-mem-001-3 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "3" + - name: gender + value: "M" + artifacts: + - name: fastq1 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: SP31.fq + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: fastq2 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: SP32.fq + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - - name: bwamem-001-4 + template: bwa-mem-001-4 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "4" + - name: gender + value: "M" + artifacts: + - name: fastq1 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: SP41.fq + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: fastq2 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: SP42.fq + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - - name: sortbyqueryname-querynamesort-001-1 + template: sort-by-queryname-001-1 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + artifacts: + - name: bwamem-alignedreads-bam-001-1 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bwamem-alignedreads-bai-001-1 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.001.1.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - - name: sortbyqueryname-querynamesort-001-2 + template: sort-by-queryname-001-2 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "2" + artifacts: + - name: bwamem-alignedreads-bam-001-2 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.001.2.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bwamem-alignedreads-bai-001-2 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.001.2.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - - name: sortbyqueryname-querynamesort-001-3 + template: sort-by-queryname-001-3 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "3" + artifacts: + - name: bwamem-alignedreads-bam-001-3 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.001.3.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bwamem-alignedreads-bai-001-3 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.001.3.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - - name: sortbyqueryname-querynamesort-001-4 + template: sort-by-queryname-001-4 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "4" + artifacts: + - name: bwamem-alignedreads-bam-001-4 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.001.4.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: bwamem-alignedreads-bai-001-4 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: alignedreads.001.4.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +## Mark Duplicates #################################################### +####################################################################### + - - name: markduplicates-001-1 + template: mark-duplicates-001-1 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + artifacts: + - name: querynamesort-alignedreads-bam-001-1 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: querynamesort-alignedreads-bai-001-1 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.001.1.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +## Mark Duplicates #################################################### +####################################################################### + - - name: markduplicates-001-2 + template: mark-duplicates-001-2 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "2" + artifacts: + - name: querynamesort-alignedreads-bam-001-2 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.001.2.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: querynamesort-alignedreads-bai-001-2 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.001.2.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +## Mark Duplicates #################################################### +####################################################################### + - - name: markduplicates-001-3 + template: mark-duplicates-001-3 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "3" + artifacts: + - name: querynamesort-alignedreads-bam-001-3 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.001.3.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: querynamesort-alignedreads-bai-001-3 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.001.3.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +## Mark Duplicates #################################################### +####################################################################### + - - name: markduplicates-001-4 + template: mark-duplicates-001-4 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "4" + artifacts: + - name: querynamesort-alignedreads-bam-001-4 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.001.4.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: querynamesort-alignedreads-bai-001-4 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: querynamesort.alignedreads.001.4.bai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +### Merge deduped BAMs, to get a single BAM file before coordinate sorting ## +####################################################################### + - - name: mergebams-001-1 + template: merge-bams-001-1 + arguments: + parameters: + - name: sampleid + value: "001" + - name: previousstepname + value: "aligned-deduped-per-lane" + artifacts: + - name: markduplicates-bam-001-1 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: dedup.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: markduplicates-bam-001-2 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: dedup.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: markduplicates-bam-001-3 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: dedup.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: markduplicates-bam-001-4 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: dedup.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reads-bam-lane2 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: dedup.001.002.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### + - - name: sortbycoordinate-coordinatesort-001-1 + template: sort-by-coordinate-001-1 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + artifacts: + - name: mergebams-bam-001-1 + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: mergebams.001.1.markduplicates.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +##### BQSR on this coordinate sorted merged BAM with RG Added ######### +####################################################################### +####################################################################### + - - name: baserecalibration-001-Interval1 + template: base-recalibration-001-Interval1 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + - name: intervalnumber + value: "Interval1" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp-tbi + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf-idx + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: intervalslist + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/cgs_exome_ace3_plusminus10bp_allcontigs.interval_list + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +##### ApplyBQSR on this coordinate sorted merged BAM with RG Added #### +####################################################################### +####################################################################### + - - name: applybqsr-001-Interval1 + template: apply-bqsr-001-Interval1 + arguments: + parameters: + - name: sampleid + value: "001" + - name: intervalnumber + value: "Interval1" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: recalibration-report + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.001.1.Interval1.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +##### BQSR on this coordinate sorted merged BAM with RG Added ######### +####################################################################### +####################################################################### + - - name: baserecalibration-001-Interval2 + template: base-recalibration-001-Interval2 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + - name: intervalnumber + value: "Interval2" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp-tbi + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf-idx + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: intervalslist + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/cgs_exome_ace3_plusminus20bp_allcontigs.interval_list + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +##### ApplyBQSR on this coordinate sorted merged BAM with RG Added #### +####################################################################### +####################################################################### + - - name: applybqsr-001-Interval2 + template: apply-bqsr-001-Interval2 + arguments: + parameters: + - name: sampleid + value: "001" + - name: intervalnumber + value: "Interval2" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: recalibration-report + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.001.1.Interval2.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +##### BQSR on this coordinate sorted merged BAM with RG Added ######### +####################################################################### +####################################################################### + - - name: baserecalibration-001-Interval3 + template: base-recalibration-001-Interval3 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + - name: intervalnumber + value: "Interval3" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp-tbi + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf-idx + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: intervalslist + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/cgs_exome_ace3_plusminus30bp_allcontigs.interval_list + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +##### ApplyBQSR on this coordinate sorted merged BAM with RG Added #### +####################################################################### +####################################################################### + - - name: applybqsr-001-Interval3 + template: apply-bqsr-001-Interval3 + arguments: + parameters: + - name: sampleid + value: "001" + - name: intervalnumber + value: "Interval3" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: recalibration-report + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.001.1.Interval3.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +##### BQSR on this coordinate sorted merged BAM with RG Added ######### +####################################################################### +####################################################################### + - - name: baserecalibration-001-Interval4 + template: base-recalibration-001-Interval4 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + - name: intervalnumber + value: "Interval4" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp-tbi + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf-idx + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: intervalslist + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/cgs_exome_ace3_plusminus40bp_allcontigs.interval_list + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +##### ApplyBQSR on this coordinate sorted merged BAM with RG Added #### +####################################################################### +####################################################################### + - - name: applybqsr-001-Interval4 + template: apply-bqsr-001-Interval4 + arguments: + parameters: + - name: sampleid + value: "001" + - name: intervalnumber + value: "Interval4" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: recalibration-report + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.001.1.Interval4.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +##### BQSR on this coordinate sorted merged BAM with RG Added ######### +####################################################################### +####################################################################### + - - name: baserecalibration-001-Interval5 + template: base-recalibration-001-Interval5 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + - name: intervalnumber + value: "Interval5" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp-tbi + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf-idx + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: intervalslist + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/cgs_exome_ace3_plusminus50bp_allcontigs.interval_list + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +##### ApplyBQSR on this coordinate sorted merged BAM with RG Added #### +####################################################################### +####################################################################### + - - name: applybqsr-001-Interval5 + template: apply-bqsr-001-Interval5 + arguments: + parameters: + - name: sampleid + value: "001" + - name: intervalnumber + value: "Interval5" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: recalibration-report + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.001.1.Interval5.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +##### BQSR on this coordinate sorted merged BAM with RG Added ######### +####################################################################### +####################################################################### + - - name: baserecalibration-001-Interval6 + template: base-recalibration-001-Interval6 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + - name: intervalnumber + value: "Interval6" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp-tbi + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf-idx + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: intervalslist + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/cgs_exome_ace3_plusminus60bp_allcontigs.interval_list + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +##### ApplyBQSR on this coordinate sorted merged BAM with RG Added #### +####################################################################### +####################################################################### + - - name: applybqsr-001-Interval6 + template: apply-bqsr-001-Interval6 + arguments: + parameters: + - name: sampleid + value: "001" + - name: intervalnumber + value: "Interval6" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: recalibration-report + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.001.1.Interval6.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +##### BQSR on this coordinate sorted merged BAM with RG Added ######### +####################################################################### +####################################################################### + - - name: baserecalibration-001-Interval7 + template: base-recalibration-001-Interval7 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + - name: intervalnumber + value: "Interval7" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp-tbi + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf-idx + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: intervalslist + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/cgs_exome_ace3_plusminus70bp_allcontigs.interval_list + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +##### ApplyBQSR on this coordinate sorted merged BAM with RG Added #### +####################################################################### +####################################################################### + - - name: applybqsr-001-Interval7 + template: apply-bqsr-001-Interval7 + arguments: + parameters: + - name: sampleid + value: "001" + - name: intervalnumber + value: "Interval7" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: recalibration-report + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.001.1.Interval7.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +##### BQSR on this coordinate sorted merged BAM with RG Added ######### +####################################################################### +####################################################################### + - - name: baserecalibration-001-Interval8 + template: base-recalibration-001-Interval8 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + - name: intervalnumber + value: "Interval8" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp-tbi + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf-idx + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: intervalslist + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/cgs_exome_ace3_plusminus80bp_allcontigs.interval_list + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +##### ApplyBQSR on this coordinate sorted merged BAM with RG Added #### +####################################################################### +####################################################################### + - - name: applybqsr-001-Interval8 + template: apply-bqsr-001-Interval8 + arguments: + parameters: + - name: sampleid + value: "001" + - name: intervalnumber + value: "Interval8" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: recalibration-report + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.001.1.Interval8.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +##### BQSR on this coordinate sorted merged BAM with RG Added ######### +####################################################################### +####################################################################### + - - name: baserecalibration-001-Interval9 + template: base-recalibration-001-Interval9 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + - name: intervalnumber + value: "Interval9" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp-tbi + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf-idx + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: intervalslist + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/cgs_exome_ace3_plusminus90bp_allcontigs.interval_list + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +##### ApplyBQSR on this coordinate sorted merged BAM with RG Added #### +####################################################################### +####################################################################### + - - name: applybqsr-001-Interval9 + template: apply-bqsr-001-Interval9 + arguments: + parameters: + - name: sampleid + value: "001" + - name: intervalnumber + value: "Interval9" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: recalibration-report + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.001.1.Interval9.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +##### BQSR on this coordinate sorted merged BAM with RG Added ######### +####################################################################### +####################################################################### + - - name: baserecalibration-001-Interval10 + template: base-recalibration-001-Interval10 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + - name: intervalnumber + value: "Interval10" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp-tbi + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf-idx + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: intervalslist + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/cgs_exome_ace3_plusminus100bp_allcontigs.interval_list + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +##### ApplyBQSR on this coordinate sorted merged BAM with RG Added #### +####################################################################### +####################################################################### + - - name: applybqsr-001-Interval10 + template: apply-bqsr-001-Interval10 + arguments: + parameters: + - name: sampleid + value: "001" + - name: intervalnumber + value: "Interval10" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: recalibration-report + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.001.1.Interval10.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +##### BQSR on this coordinate sorted merged BAM with RG Added ######### +####################################################################### +####################################################################### + - - name: baserecalibration-001-Interval11 + template: base-recalibration-001-Interval11 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + - name: intervalnumber + value: "Interval11" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp-tbi + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf-idx + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: intervalslist + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/cgs_exome_ace3_plusminus110bp_allcontigs.interval_list + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +##### ApplyBQSR on this coordinate sorted merged BAM with RG Added #### +####################################################################### +####################################################################### + - - name: applybqsr-001-Interval11 + template: apply-bqsr-001-Interval11 + arguments: + parameters: + - name: sampleid + value: "001" + - name: intervalnumber + value: "Interval11" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: recalibration-report + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.001.1.Interval11.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +##### BQSR on this coordinate sorted merged BAM with RG Added ######### +####################################################################### +####################################################################### + - - name: baserecalibration-001-Interval12 + template: base-recalibration-001-Interval12 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + - name: intervalnumber + value: "Interval12" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp-tbi + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf-idx + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: intervalslist + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/cgs_exome_ace3_plusminus120bp_allcontigs.interval_list + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +##### ApplyBQSR on this coordinate sorted merged BAM with RG Added #### +####################################################################### +####################################################################### + - - name: applybqsr-001-Interval12 + template: apply-bqsr-001-Interval12 + arguments: + parameters: + - name: sampleid + value: "001" + - name: intervalnumber + value: "Interval12" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: recalibration-report + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.001.1.Interval12.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey +####################################################################### +##### BQSR on this coordinate sorted merged BAM with RG Added ######### +####################################################################### +####################################################################### + - - name: baserecalibration-001-Interval13 + template: base-recalibration-001-Interval13 + arguments: + parameters: + - name: sampleid + value: "001" + - name: laneid + value: "1" + - name: intervalnumber + value: "Interval13" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: dbsnp-tbi + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/dbSNP.b151.GRCh37p13.All_2018.vcf.gz.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: gold-standard-indels-vcf-idx + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/Mills_and_1000G_gold_standard.indels.vcf.tbi + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey + - name: intervalslist + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/cgs_exome_ace3_plusminus130bp_allcontigs.interval_list + accesskeySecret: + name: storage-credentials + key: accesskey + secretkeySecret: + name: storage-credentials + key: secretkey +####################################################################### +####################################################################### +##### ApplyBQSR on this coordinate sorted merged BAM with RG Added #### +####################################################################### +####################################################################### + - - name: applybqsr-001-Interval13 + template: apply-bqsr-001-Interval13 + arguments: + parameters: + - name: sampleid + value: "001" + - name: intervalnumber + value: "Interval13" + artifacts: + - name: coordinatesort-bam + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: coordinatesort.001.1.bam + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: recalibration-report + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: bqsr.recalibration.001.1.Interval13.table + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-sa + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.sa + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-pac + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.pac + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fai + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.fai + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-bwt + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.bwt + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-ann + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.ann + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-amb + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta.amb + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-fasta + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.fasta + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey + - name: reference-files-dict + s3: + endpoint: storage.googleapis.com + bucket: test-argo-artifacts + key: tmp/chr21/human_g1k_v37_decoy.21.dict + accessKeySecret: + name: storage-credentials + key: accesskey + secretKeySecret: + name: storage-credentials + key: secretkey diff --git a/build.number b/build.number new file mode 100644 index 0000000..4fbd40c --- /dev/null +++ b/build.number @@ -0,0 +1,3 @@ +#Build Number for ANT. Do not edit! +#Thu Jan 16 20:26:23 PST 2020 +build.number=5 diff --git a/build.xml b/build.xml new file mode 100644 index 0000000..a678a03 --- /dev/null +++ b/build.xml @@ -0,0 +1,106 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/javadoc.xml b/javadoc.xml new file mode 100644 index 0000000..2e69326 --- /dev/null +++ b/javadoc.xml @@ -0,0 +1,14 @@ + + + + + + + + + + + + + +