Re-branding nf-seqqc to bacpaq #61

anwarMZ · 2024-04-08T05:42:13Z

No description provided.

anwarMZ · 2024-04-08T05:44:20Z

@jimmyliu1326 there is a lot of information here - let's try to go over it in this thread and solve it sequentially.

jimmyliu1326 · 2024-04-09T02:05:48Z

Documenting discussion points as I go through the PR:

Dehosting is removing all the bacterial reads
The recommended method to run the workflow is by referencing the Github release i.e. nextflow run cidgoh/bac-pac -r [release]
Consistent pipeline naming bacpaq or bac-paq
ERROR ~ Failed to invoke workflow.onComplete event handler
Sample sheet validation scheme schema_input.json is incompatible with assembled genome and nanopore data inputs
Missing parameters in nextflow_schema.json e.g. workflow
Printing pipeline version requires user to supply a valid profile

… in same samplesheet

…ity for short and long reads

jimmyliu1326 · 2024-05-11T03:56:19Z

Keeping track of the progress on the aforementioned issues:

Dehosting is removing all the bacterial reads c96a7ea
The recommended method to run the workflow is by referencing the Github release i.e. nextflow run cidgoh/bac-pac -r [release]
Consistent pipeline naming bacpaq or bac-paq
ERROR ~ Failed to invoke workflow.onComplete event handler
Sample sheet validation scheme schema_input.json is incompatible with assembled genome and nanopore data inputs cfbe66e
Missing parameters in nextflow_schema.json e.g. workflow
Printing pipeline version requires user to supply a valid profile a6dd605
File name conflict between Illumina and Nanopore genome assembly when publishing to output directory

github-actions · 2024-05-31T17:43:51Z

`nf-core lint` overall result: Failed ❌

Posted for pipeline commit 9cb326c

+| ✅ 223 tests passed       |+
!| ❗  84 tests had warnings |!
-| ❌  86 tests failed       |-

❌ Test failures:

files_exist - File must be removed: lib/Utils.groovy
files_exist - File not found check: lib/nfcore_external_java_deps.jar
nextflow_config - Config variable not found: params.validationShowHiddenParams
nextflow_config - Config variable not found: params.validationSchemaIgnoreParams
nextflow_config - Config manifest.name did not begin with nf-core/:
cidgoh/bacpaq
nextflow_config - Config variable manifest.homePage did not begin with https://github.com/nf-core/:
https://github.com/cidgoh/bacpaq
nextflow_config - Config default value incorrect: params.mode is set as illumina in nextflow_schema.json but is nanopore in nextflow.config.
nextflow_config - Config default value incorrect: params.skip_subsampling is set as true in nextflow_schema.json but is false in nextflow.config.
nextflow_config - Config default value incorrect: params.depth_cut_off is set as 50,80 in nextflow_schema.json but is 50 in nextflow.config.
nextflow_config - Default value from the Nextflow schema params.tracedir = 25.MB`` not found in nextflow.config.
nextflow_config - Config default value incorrect: params.validate_params is set as true in nextflow_schema.json but is false in nextflow.config.
nextflow_config - Config default value incorrect: params.schema_ignore_params is set as fasta in nextflow_schema.json but is genomes in nextflow.config.
files_unchanged - .github/CONTRIBUTING.md does not match the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml does not match the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml does not match the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
files_unchanged - .github/workflows/branch.yml does not match the template
files_unchanged - .github/workflows/linting_comment.yml does not match the template
files_unchanged - .github/workflows/linting.yml does not match the template
files_unchanged - assets/email_template.html does not match the template
files_unchanged - assets/email_template.txt does not match the template
files_unchanged - assets/sendmail_template.txt does not match the template
files_unchanged - docs/README.md does not match the template
actions_ci - Minimum pipeline NF version '22.01.0' is not tested in '.github/workflows/ci.yml'
readme - README Nextflow minimum version badge does not match config. Badge: 23.04.0, Config: 22.01.0
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/modules/local/RMLST/ubuntu_curl_test.sif L319578: b{{XmwçDç�Ë{«=4�¼Ö¶?fÍÛp�Õ}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-angular.mjs L2: "{{","}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-angular.mjs L2: "{{",I="}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L6: "{{{",e.strip.open&&(this.buffer+="~~"),this.Expression(e.path),this.Params(e.params),this.Hash(e.hash),e.strip.close&&(this.buffer+="~~"),this.buffer+=e.escaped?"}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L6: "{{#",this.Expression(e.path),this.Params(e.params),this.Hash(e.hash),e.program.blockParams.length&&this.BlockParams(e.program.blockParams),e.chained?this.buffer+=e.inverseStrip.close?"~}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L6: "{{",this.buffer+="else",this.buffer+=e.inverseStrip.close?"~}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L6: "{{/",this.Expression(e.path),this.buffer+=e.closeStrip.close?"~}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L6: "{{>",this.Expression(e.name),this.Params(e.params),this.Hash(e.hash),this.buffer+="}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L6: "{{",this.Expression(e.path),this.Params(e.params),this.Hash(e.hash),this.buffer+="}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L12: "{{ "+this.SubExpression(l)+" }}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L12: "{{ DIRECTIVE "+this.SubExpression(l)+" }}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L12: "{{^}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L12: "{{> "+e+" }}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L12: "{{> "+e+" }}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L12: "{{! '"+l.value+"' }}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L26: `{{${(0,c.printLiteral)(b)}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L27: ({{> ...}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L27: `{{#${M.path}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-glimmer.mjs L27: `{{#${C.path}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-html.mjs L34: "{{","}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-html.mjs L35: "{{ '{' }}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/parser-markdown.mjs L75: |{{.*?}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/standalone.mjs L75: "{{",Re(H,X),"}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/standalone.mjs L107: /{{(.+?)}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/standalone.mjs L110: /{{(.+?)}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/esm/standalone.mjs L110: "{{",d(Z),"}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/index.js L32245: "{{", printPathAndParams(path, print2), "}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/index.js L35748: /{{(.+?)}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/index.js L36588: /{{(.+?)}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/index.js L36602: "{{", replaceTextEndOfLine(part), "}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-angular.js L2: "{{","}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-angular.js L2: "{{",I="}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L6: "{{{",e.strip.open&&(this.buffer+="~~"),this.Expression(e.path),this.Params(e.params),this.Hash(e.hash),e.strip.close&&(this.buffer+="~~"),this.buffer+=e.escaped?"}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L6: "{{#",this.Expression(e.path),this.Params(e.params),this.Hash(e.hash),e.program.blockParams.length&&this.BlockParams(e.program.blockParams),e.chained?this.buffer+=e.inverseStrip.close?"~}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L6: "{{",this.buffer+="else",this.buffer+=e.inverseStrip.close?"~}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L6: "{{/",this.Expression(e.path),this.buffer+=e.closeStrip.close?"~}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L6: "{{>",this.Expression(e.name),this.Params(e.params),this.Hash(e.hash),this.buffer+="}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L6: "{{",this.Expression(e.path),this.Params(e.params),this.Hash(e.hash),this.buffer+="}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L12: "{{ "+this.SubExpression(o)+" }}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L12: "{{ DIRECTIVE "+this.SubExpression(o)+" }}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L12: "{{^}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L12: "{{> "+e+" }}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L12: "{{> "+e+" }}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L12: "{{! '"+o.value+"' }}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L26: `{{${(0,c.printLiteral)(b)}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L27: ({{> ...}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L27: `{{#${M.path}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-glimmer.js L27: `{{#${C.path}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-html.js L34: "{{","}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-html.js L35: "{{ '{' }}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/parser-markdown.js L75: |{{.*?}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/standalone.js L75: "{{",Re(H,X),"}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/standalone.js L107: /{{(.+?)}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/standalone.js L110: /{{(.+?)}}
template_strings - Found a Jinja template string in /home/runner/work/nf-seqqc/nf-seqqc/node_modules/prettier/standalone.js L110: "{{",y(Z),"}}
schema_params - Default value for param skip_subsampling invalid: Schema default (True) does not match the config default (false)
schema_params - Default value for param tracedir invalid: Not in pipeline parameters. Check nextflow.config.
schema_params - Default value for param validate_params invalid: Schema default (True) does not match the config default (false)
multiqc_config - assets/multiqc_config.yml does not meet requirements: Section cidgoh-bacpaq-summary missing in report_section_order
modules_config - conf/modules.config contains withName:MINIMAP2_ILLUMINA, but the corresponding process is not present in any of the Nextflow scripts.
modules_config - conf/modules.config contains withName:MINIMAP2_NANOPORE, but the corresponding process is not present in any of the Nextflow scripts.

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
schema_lint - Schema $id should be https://raw.githubusercontent.com/cidgoh/bacpaq/master/nextflow_schema.json
Found https://raw.githubusercontent.com/nf-core/bacpaq/master/nextflow_schema.json
schema_params - Schema param tracedir not found from nextflow config
schema_description - Ungrouped param in schema: fasta
schema_description - No description provided in schema for parameter: adapter_fasta
schema_description - No description provided in schema for parameter: skip_subsampling
schema_description - No description provided in schema for parameter: skip_confindr
schema_description - No description provided in schema for parameter: save_merged
schema_description - No description provided in schema for parameter: trim_tool
schema_description - No description provided in schema for parameter: save_trimmed_fail
schema_description - No description provided in schema for parameter: depth_cut_off
schema_description - No description provided in schema for parameter: confindr_db
schema_description - No description provided in schema for parameter: skip_QC
schema_description - No description provided in schema for parameter: skip_raw_qc
schema_description - No description provided in schema for parameter: subsampling_genomesize
schema_description - No description provided in schema for parameter: classifier
schema_description - No description provided in schema for parameter: skip_combinekreports
schema_description - No description provided in schema for parameter: skip_kreport2krona
schema_description - No description provided in schema for parameter: skip_bracken
schema_description - No description provided in schema for parameter: skip_kraken2
schema_description - No description provided in schema for parameter: skip_combinebrackenoutputs
schema_description - No description provided in schema for parameter: skip_dehosting
schema_description - No description provided in schema for parameter: kraken2_db
schema_description - No description provided in schema for parameter: classified_reads
schema_description - No description provided in schema for parameter: unclassified_reads
schema_description - No description provided in schema for parameter: centrifuge_db
schema_description - No description provided in schema for parameter: save_unaligned
schema_description - No description provided in schema for parameter: save_aligned
schema_description - No description provided in schema for parameter: dehosting_aligner
schema_description - No description provided in schema for parameter: sam_format
schema_description - No description provided in schema for parameter: bam_format
schema_description - No description provided in schema for parameter: bwa_sort_bam
schema_description - No description provided in schema for parameter: cigar_paf_format
schema_description - No description provided in schema for parameter: cigar_bam
schema_description - No description provided in schema for parameter: interleaved
schema_description - No description provided in schema for parameter: host_genome
schema_description - No description provided in schema for parameter: host_genome_id
schema_description - No description provided in schema for parameter: skip_taxonomy_qc
schema_description - No description provided in schema for parameter: min_contig_len
schema_description - No description provided in schema for parameter: min_contig_coverage
schema_description - No description provided in schema for parameter: min_input_read_len
schema_description - No description provided in schema for parameter: min_input_quality
schema_description - No description provided in schema for parameter: racon_rounds
schema_description - No description provided in schema for parameter: medaka_rounds
schema_description - No description provided in schema for parameter: medaka_model
schema_description - No description provided in schema for parameter: sr_assembler
schema_description - No description provided in schema for parameter: skip_assembly
schema_description - No description provided in schema for parameter: assembly_genomesize
schema_description - No description provided in schema for parameter: checkm_db
schema_description - No description provided in schema for parameter: combine_quast
schema_description - No description provided in schema for parameter: busco_lineage
schema_description - No description provided in schema for parameter: busco_lineages_path
schema_description - No description provided in schema for parameter: busco_config
schema_description - No description provided in schema for parameter: skip_checkm
schema_description - No description provided in schema for parameter: skip_quast
schema_description - No description provided in schema for parameter: skip_busco
schema_description - No description provided in schema for parameter: reference_genome_fasta
schema_description - No description provided in schema for parameter: reference_genome_gff
schema_description - No description provided in schema for parameter: skip_assembly_qc
schema_description - No description provided in schema for parameter: skip_rmlst
schema_description - No description provided in schema for parameter: skip_gene_annotation
schema_description - No description provided in schema for parameter: skip_prokka
schema_description - No description provided in schema for parameter: skip_bakta
schema_description - No description provided in schema for parameter: bakta_db
schema_description - No description provided in schema for parameter: prodigal_training_file
schema_description - No description provided in schema for parameter: annotation_protein_file
schema_description - No description provided in schema for parameter: skip_pangenome_analysis
schema_description - No description provided in schema for parameter: pangenome_input
schema_description - No description provided in schema for parameter: skip_roary
schema_description - No description provided in schema for parameter: skip_pirate
schema_description - No description provided in schema for parameter: skip_panaroo
schema_description - No description provided in schema for parameter: skip_peppan
schema_description - No description provided in schema for parameter: clean_mode
schema_description - No description provided in schema for parameter: reference_gff
schema_description - No description provided in schema for parameter: skip_plasmid_analysis
schema_description - No description provided in schema for parameter: skip_plasmidfinder
schema_description - No description provided in schema for parameter: skip_mobsuite
schema_description - No description provided in schema for parameter: skip_phage_annotation
schema_description - No description provided in schema for parameter: virsorter_db
schema_description - No description provided in schema for parameter: virsorter_virus_grp
schema_description - No description provided in schema for parameter: virsorter_min_len
schema_description - No description provided in schema for parameter: virsorter_min_score
schema_description - No description provided in schema for parameter: skip_cctyper
nfcore_yml - nf-core version not set in .nf-core.yml

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-bacpaq_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-bacpaq_logo_light.png
files_exist - File found: docs/images/nf-core-bacpaq_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-bacpaq_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowBacpaq.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 1.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.fasta= test.fa
nextflow_config - Config default value correct: params.nanopore_summary_file_id= test
nextflow_config - Config default value correct: params.adapter_fasta= https://object-arbutus.cloud.computecanada.ca/cidgohshare/database/adaptors/test.fa
nextflow_config - Config default value correct: params.save_merged= true
nextflow_config - Config default value correct: params.trim_tool= fastp
nextflow_config - Config default value correct: params.confindr_db= /mnt/cidgoh-object-storage/database/confindr/confindr_db
nextflow_config - Config default value correct: params.subsampling_genomesize= 5000000
nextflow_config - Config default value correct: params.classifier= kraken2
nextflow_config - Config default value correct: params.kraken2_db= /mnt/cidgoh-object-storage/database/minikraken2/minikraken2_v2_8GB_201904_UPDATE
nextflow_config - Config default value correct: params.classified_reads= true
nextflow_config - Config default value correct: params.unclassified_reads= true
nextflow_config - Config default value correct: params.centrifuge_db= /mnt/cidgoh-object-storage/database/centrifuge
nextflow_config - Config default value correct: params.save_unaligned= true
nextflow_config - Config default value correct: params.save_aligned= true
nextflow_config - Config default value correct: params.dehosting_aligner= minimap2
nextflow_config - Config default value correct: params.sam_format= true
nextflow_config - Config default value correct: params.bam_format= true
nextflow_config - Config default value correct: params.bwa_sort_bam= sort
nextflow_config - Config default value correct: params.host_genome= /mnt/cidgoh-object-storage/database/reference_genomes/human/GRCh38.p14/GCF_000001405.40/GCF_000001405.40_GRCh38.p14_genomic.fna
nextflow_config - Config default value correct: params.host_genome_id= GRCh38
nextflow_config - Config default value correct: params.min_contig_len= 500
nextflow_config - Config default value correct: params.min_contig_coverage= 2
nextflow_config - Config default value correct: params.min_input_read_len= 1000
nextflow_config - Config default value correct: params.min_input_quality= 0
nextflow_config - Config default value correct: params.racon_rounds= 1
nextflow_config - Config default value correct: params.medaka_rounds= 1
nextflow_config - Config default value correct: params.medaka_model= r941_min_fast_g507
nextflow_config - Config default value correct: params.sr_assembler= spades
nextflow_config - Config default value correct: params.assembly_genomesize= '\
nextflow_config - Config default value correct: params.busco_lineage= bacteria
nextflow_config - Config default value correct: params.busco_lineages_path= /mnt/cidgoh-object-storage/database/busco
nextflow_config - Config default value correct: params.bakta_db= /mnt/cidgoh-object-storage/database/bakta/db/
nextflow_config - Config default value correct: params.pangenome_input= bakta
nextflow_config - Config default value correct: params.clean_mode= moderate
nextflow_config - Config default value correct: params.virsorter_virus_grp= dsDNAphage,ssDNA
nextflow_config - Config default value correct: params.virsorter_min_len= 5000
nextflow_config - Config default value correct: params.virsorter_min_score= 0.4
nextflow_config - Config default value correct: params.abricate_db= card
nextflow_config - Config default value correct: params.resfinder_species= ecoli
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
schema_lint - Schema lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - SAMPLESHEET_CHECK found in conf/modules.config and Nextflow scripts.
modules_config - CAT_NANOPORE_FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - PORECHOP_ABI found in conf/modules.config and Nextflow scripts.
modules_config - NANOCOMP found in conf/modules.config and Nextflow scripts.
modules_config - PYCOQC found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - RAW_FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - TRIM_FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - RAW_MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - TRIM_MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - TRIMMOMATIC found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
modules_config - DRAGONFLYE found in conf/modules.config and Nextflow scripts.
modules_config - SHOVILL found in conf/modules.config and Nextflow scripts.
modules_config - RENAME_CTG found in conf/modules.config and Nextflow scripts.
modules_config - QUAST found in conf/modules.config and Nextflow scripts.
modules_config - QUAST found in conf/modules.config and Nextflow scripts.
modules_config - BUSCO found in conf/modules.config and Nextflow scripts.
modules_config - RMLST found in conf/modules.config and Nextflow scripts.
modules_config - RMLSTPARSE found in conf/modules.config and Nextflow scripts.
modules_config - PROKKA found in conf/modules.config and Nextflow scripts.
modules_config - BAKTA_BAKTADBDOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - BAKTA_BAKTA found in conf/modules.config and Nextflow scripts.
modules_config - VIRSORTER2_RUN found in conf/modules.config and Nextflow scripts.
modules_config - VIRSORTER2_SETUP found in conf/modules.config and Nextflow scripts.
modules_config - PANAROO_RUN found in conf/modules.config and Nextflow scripts.
modules_config - ROARY found in conf/modules.config and Nextflow scripts.
modules_config - PIRATE found in conf/modules.config and Nextflow scripts.
modules_config - PEPPAN found in conf/modules.config and Nextflow scripts.
modules_config - MOBSUITE_RECON found in conf/modules.config and Nextflow scripts.
modules_config - PLASMIDFINDER found in conf/modules.config and Nextflow scripts.
modules_config - RESFINDER found in conf/modules.config and Nextflow scripts.
modules_config - ABRICATE_RUN found in conf/modules.config and Nextflow scripts.
modules_config - ABRICATE_SUMMARY found in conf/modules.config and Nextflow scripts.
modules_config - AMRFINDERPLUS_UPDATE found in conf/modules.config and Nextflow scripts.
modules_config - AMRFINDERPLUS_RUN found in conf/modules.config and Nextflow scripts.
modules_config - RGI_MAIN found in conf/modules.config and Nextflow scripts.
modules_config - ABRITAMR_RUN found in conf/modules.config and Nextflow scripts.
modules_config - CCTYPER found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline

Run details

nf-core/tools version 2.14.1
Run at 2024-05-31 21:13:20

anwarMZ added 11 commits April 2, 2024 21:33

updating name

a42f9d0

update name

13c2035

update name

eb9db73

Template update for nf-core/tools version 2.13.1

a062ea3

updated README

5766a44

converting workflows to sub-workflows

5205bb5

new high-level workflow

247007f

updated main.nf with new strcuture

3ae76c8

updated modules

c46e528

updated utils

f024c4e

Merge branch 'dev' into change_name

0d993e1

anwarMZ added the re-branding label Apr 8, 2024

anwarMZ requested a review from jimmyliu1326 April 8, 2024 05:42

jimmyliu1326 added 3 commits April 8, 2024 18:05

disable input check in subworkflows

c6752e7

add func to print pipeline vers

f1efd0c

remove redundant profiles

3305e65

jimmyliu1326 and others added 12 commits April 8, 2024 19:53

add container options to prevent conflict with local libs

a726178

remove version printing, already handled by nf-plguins

ec01d30

define ch_input

bf02c58

updated the input schema to allow fastq1, fast2, fastq_dir and genome…

3a57bc2

… in same samplesheet

workflow input compatibility with nf-validation

28bebb8

updating regex pattern for genome file

57c43bf

update input set mapping

9c45d9d

update input set mapping

e04a808

moving from input_check to nf-validation

4a8f065

updating the sub-woirflow to follow nf-valdiation and adding flexibil…

cfbe66e

…ity for short and long reads

updating bacpaq for nf-valdiation

cf299f3

cleanup for nf-validation structure

e68bdbf

jimmyliu1326 added 4 commits May 10, 2024 20:35

use dynamic directive for minimap_align

3e464c0

set validate params to off by default

a6dd605

fixed interleaved emitted as value channel

c96a7ea

fixed branching after raw read and taxonomy qc

ee4d476

jimmyliu1326 added 2 commits May 31, 2024 10:36

update manifest

e8c5643

standardize pipeline name

4a568e6

jimmyliu1326 and others added 9 commits May 31, 2024 11:05

update nextflow run cmds

b086a6e

remove irrelevant texts

4ab580d

isolated dirs for lr and sr assembly

9288fe3

use nf-core/rasusa

f7e40f1

format updated

5499f49

fixed error with reference gff

6524f86

archived rasusa local

012a608

updated the extensions for genomes

2016f08

dumpsoftwareversion added

9cb326c

jimmyliu1326 approved these changes May 31, 2024

View reviewed changes

anwarMZ merged commit ee42604 into dev May 31, 2024
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Re-branding nf-seqqc to bacpaq #61

Re-branding nf-seqqc to bacpaq #61

anwarMZ commented Apr 8, 2024

anwarMZ commented Apr 8, 2024

jimmyliu1326 commented Apr 9, 2024 •

edited

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jimmyliu1326 commented May 11, 2024 •

edited by anwarMZ

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github-actions bot commented May 31, 2024 •

edited

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❌ Test failures:

❗ Test warnings:

✅ Tests passed:

Run details

Re-branding nf-seqqc to bacpaq #61

Re-branding nf-seqqc to bacpaq #61

Conversation

anwarMZ commented Apr 8, 2024

anwarMZ commented Apr 8, 2024

jimmyliu1326 commented Apr 9, 2024 • edited Loading

jimmyliu1326 commented May 11, 2024 • edited by anwarMZ Loading

github-actions bot commented May 31, 2024 • edited Loading

nf-core lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

✅ Tests passed:

Run details

jimmyliu1326 commented Apr 9, 2024 •

edited

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jimmyliu1326 commented May 11, 2024 •

edited by anwarMZ

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github-actions bot commented May 31, 2024 •

edited

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`nf-core lint` overall result: Failed ❌