Merge pull request #17 from TRON-Bioinformatics/add-ci-profile

Added CI profile and update conda profile

Author: LKress

nextflow.config

@@ -5,18 +5,23 @@
  */
 
 profiles {
-  conda { params.enable_conda = true }
+  conda { 
+    params.enable_conda = true
+    conda.enabled = true
+  }
   debug { process.beforeScript = 'echo $HOSTNAME' }
-  test {
-    params.reference = "$baseDir/test/data/ucsc.hg19.minimal.fasta"
-    params.input_vcfs = "$baseDir/test/data/test_input.txt"
+  ci {
     params.cpus = 1
     params.memory = "3g"
     timeline.enabled = false
     report.enabled = false
     trace.enabled = false
     dag.enabled = false
   }
+  test {
+    params.reference = "$baseDir/test/data/ucsc.hg19.minimal.fasta"
+    params.input_vcfs = "$baseDir/test/data/test_input.txt"
+  }
 }
 
 // Export this variable to prevent local Python libraries from conflicting with those in the container

test/scripts/run_test_0.sh

@@ -4,8 +4,8 @@ output_folder=test/output/test0
 
 nextflow main.nf --help
 
-nextflow main.nf -profile test,conda --output $output_folder --skip_normalization
+nextflow main.nf -profile test,conda,ci --output $output_folder --skip_normalization
 
 # missing SNpEff data folder
-nextflow main.nf -profile test,conda --output $output_folder --snpeff_organism hg19
+nextflow main.nf -profile test,conda,ci --output $output_folder --snpeff_organism hg19
 test ! -d $output_folder

test/scripts/run_test_1.sh

@@ -4,7 +4,7 @@
 source test/scripts/assert.sh
 output_folder=test/output/test1
 
-nextflow main.nf -profile test,conda --output $output_folder
+nextflow main.nf -profile test,conda,ci --output $output_folder
 
 test -s $output_folder/single_sample/single_sample.normalized.vcf || { echo "Missing test 1 output file!"; exit 1; }
 test -s $output_folder/tumor_normal/tumor_normal.normalized.vcf || { echo "Missing test 1 output file!"; exit 1; }

test/scripts/run_test_2.sh

@@ -3,7 +3,7 @@
 
 source test/scripts/assert.sh
 output_folder=test/output/test2
-nextflow main.nf -profile test,conda --output $output_folder --filter PASS,MNV
+nextflow main.nf -profile test,conda,ci --output $output_folder --filter PASS,MNV
 test -s $output_folder/single_sample/single_sample.normalized.vcf || { echo "Missing test 2 output file!"; exit 1; }
 test -s $output_folder/tumor_normal/tumor_normal.normalized.vcf || { echo "Missing test 2 output file!"; exit 1; }
 assert_eq `wc -l $output_folder/single_sample/single_sample.normalized.vcf | cut -d' ' -f 1` 34 "Wrong number of variants"

test/scripts/run_test_3.sh

@@ -3,7 +3,7 @@
 
 source test/scripts/assert.sh
 output_folder=test/output/test3
-nextflow main.nf -profile test,conda --output $output_folder --skip_decompose_complex
+nextflow main.nf -profile test,conda,ci --output $output_folder --skip_decompose_complex
 test -s $output_folder/single_sample/single_sample.normalized.vcf || { echo "Missing test 2 output file!"; exit 1; }
 test -s $output_folder/tumor_normal/tumor_normal.normalized.vcf || { echo "Missing test 2 output file!"; exit 1; }
 assert_eq `wc -l $output_folder/single_sample/single_sample.normalized.vcf | cut -d' ' -f 1` 47 "Wrong number of variants"

test/scripts/run_test_4.sh

@@ -3,6 +3,6 @@
 
 source test/scripts/assert.sh
 output_folder=test/output/test4
-nextflow main.nf -profile test,conda --input_vcfs test/data/test_input_no_ad.txt --output $output_folder
+nextflow main.nf -profile test,conda,ci --input_vcfs test/data/test_input_no_ad.txt --output $output_folder
 test -s $output_folder/sample_no_ad/sample_no_ad.normalized.vcf || { echo "Missing test 4 output file!"; exit 1; }
 assert_eq `wc -l $output_folder/sample_no_ad/sample_no_ad.normalized.vcf | cut -d' ' -f 1` 52 "Wrong number of variants"

test/scripts/run_test_5.sh

@@ -3,6 +3,6 @@
 
 source test/scripts/assert.sh
 output_folder=test/output/test5
-nextflow main.nf -profile test,conda --output $output_folder --input_vcfs false --input_vcf test/data/test_single_sample.vcf
+nextflow main.nf -profile test,conda,ci --output $output_folder --input_vcfs false --input_vcf test/data/test_single_sample.vcf
 test -s $output_folder/test_single_sample/test_single_sample.normalized.vcf || { echo "Missing test 4 output file!"; exit 1; }
 assert_eq `wc -l $output_folder/test_single_sample/test_single_sample.normalized.vcf | cut -d' ' -f 1` 53 "Wrong number of variants"

test/scripts/run_test_6.sh

@@ -13,7 +13,7 @@ echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test/data
 echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test/data/test_bams.txt
 
 # run
-nextflow main.nf -profile test,conda --output $output_folder --input_bams test/data/test_bams.txt
+nextflow main.nf -profile test,conda,ci --output $output_folder --input_bams test/data/test_bams.txt
 
 # check results
 test -s $output_folder/single_sample/single_sample.normalized.vcf || { echo "Missing test 6 output file!"; exit 1; }

test/scripts/run_test_7.sh

@@ -9,7 +9,7 @@ echo -e "single_sample\ttumor:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test/data/
 echo -e "single_sample\ttumor:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test/data/test_bams.txt
 echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test/data/test_bams.txt
 echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test/data/test_bams.txt
-nextflow main.nf -profile test,conda --output $output_folder --input_bams test/data/test_bams.txt --skip_multiallelic_filter
+nextflow main.nf -profile test,conda,ci --output $output_folder --input_bams test/data/test_bams.txt --skip_multiallelic_filter
 test -s $output_folder/single_sample/single_sample.normalized.vcf || { echo "Missing test 7 output file!"; exit 1; }
 test -s $output_folder/tumor_normal/tumor_normal.normalized.vcf || { echo "Missing test 7 output file!"; exit 1; }
 test -s $output_folder/single_sample/single_sample.vaf.vcf || { echo "Missing test 7 output file!"; exit 1; }

test/scripts/run_test_8.sh

@@ -11,7 +11,7 @@ echo -e "single_sample\ttumor:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test/data/
 echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test/data/test_bams.txt
 echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test/data/test_bams.txt
 
-nextflow main.nf -profile test,conda --output $output_folder --input_bams test/data/test_bams.txt
+nextflow main.nf -profile test,conda,ci --output $output_folder --input_bams test/data/test_bams.txt
 
 test -s $output_folder/single_sample/single_sample.normalized.vcf || { echo "Missing test 8 output file!"; exit 1; }
 test -s $output_folder/tumor_normal/tumor_normal.normalized.vcf || { echo "Missing test 8 output file!"; exit 1; }

test/scripts/run_test_9.sh

@@ -5,7 +5,7 @@ source test/scripts/assert.sh
 output_folder=test/output/test9
 snpeff_datadir=/home/you/snpeff
 
-nextflow main.nf -profile test,conda --output $output_folder --snpeff_organism hg19 --snpeff_datadir $snpeff_datadir
+nextflow main.nf -profile test,conda,ci --output $output_folder --snpeff_organism hg19 --snpeff_datadir $snpeff_datadir
 
 test -s $output_folder/single_sample/single_sample.normalized.vcf || { echo "Missing test 1 output file!"; exit 1; }
 test -s $output_folder/tumor_normal/tumor_normal.normalized.vcf || { echo "Missing test 1 output file!"; exit 1; }