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Add handling of output_bam param #316

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Add handling of output_bam param #316

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weaglesBio
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

Added handling of additional parameter in .yaml 'output_bam'. This will have the value 'true' or 'false'. If true, the merged bam will be output to hic_files directory.

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github-actions bot commented Aug 22, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 20892da

+| ✅ 127 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.1.1'
  • pipeline_todos - TODO string in methods_description_template.yml: ## Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • system_exit - System.exit in WorkflowTreeval.groovy: System.exit(1) [line 17]

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_dark.png
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/treeval/treeval/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-08-22 15:12:30

@DLBPointon
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DLBPointon commented Aug 22, 2024 •
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As posted on Slack, I have this running locally.

    withName: '.*:.*:.*:HIC_BWAMEM2:SAMTOOLS_MERGE|.*:.*:.*:HIC_MINIMAP2:SAMTOOLS_MERGE' {
        publishDir = [
            path: { "${params.outdir}/mapped_bam" },
            mode: params.publish_dir_mode,
            saveAs: { filename -> if ${bam.size()} < 4000000000 ? null : filename }
        ]
    }

EDIT: the idea above is sound but how i implemented it was wrong

Below from slack:
Actually that's wrong isn't it you want the input genome as the comparator (edited)

Add reference.size() as a meta value in the workflows and then use that in the above instead of the bam

To really limit it you can also add a specific arg.prefix to the modules.config for these two processes and then search output file on

if filename.contains("thingmabob") && ${meta.ref_size} > 4000000000 ? filename : null

@weaglesBio weaglesBio closed this Sep 17, 2024
@weaglesBio weaglesBio deleted the output_bam branch September 17, 2024 13:13
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@yumisims yumisims Awaiting requested review from yumisims

@DLBPointon DLBPointon Awaiting requested review from DLBPointon

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@weaglesBio @DLBPointon