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add CI for --skip_markduplicates#412

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maxulysse merged 13 commits intonf-core:devfrom
maxulysse:dsl2_csv_magic
Aug 4, 2021
Merged

add CI for --skip_markduplicates#412
maxulysse merged 13 commits intonf-core:devfrom
maxulysse:dsl2_csv_magic

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@maxulysse maxulysse commented Jul 19, 2021

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • 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).

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github-actions bot commented Jul 19, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 275b066

+| ✅ 135 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  12 tests had warnings |!
Details

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
  • pipeline_todos - TODO string in main.nf: List additional required output channels/values here
  • pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable
  • pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
  • pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
  • pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-07-28 08:54:50

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maxulysse commented Jul 21, 2021

In the end I changed idea, since the mapped bams have no index, I used the merged bams when skipping markduplicates to restart from the csv file.
I'll be continuing on that theme in this PR.

@maxulysse maxulysse mentioned this pull request Jul 28, 2021
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@maxulysse maxulysse changed the base branch from dsl2 to dev August 3, 2021 13:46
FriederikeHanssen
FriederikeHanssen reviewed Aug 4, 2021
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Before approving, just want to briefly discuss when BAMQC should be run. I would have proposed after duplciate marking, if duplicate marking is skipped then after mapping.

subworkflows/nf-core/mapping.nf
// MarkDuplicates can handle multiple BAMS as input, so no merging/indexing at this step
// Except if and only if skipping MarkDuplicates

if (skip_markduplicates) {
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Ah yes, adding it here makes sense. I struggled finding a logical way on how to sort all the different ways how to walk through to base recalibration

@maxulysse @FriederikeHanssen
Update subworkflows/nf-core/qc_markduplicates.nf
4d55e71 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
@maxulysse maxulysse merged commit 2fc03e5 into nf-core:dev Aug 4, 2021
@maxulysse maxulysse deleted the dsl2_csv_magic branch August 4, 2021 12:40
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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