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Add samplesheet generation and improve usage documentation #236

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merged 10 commits into from
Aug 10, 2024
Merged

Add samplesheet generation and improve usage documentation #236

merged 10 commits into from
Aug 10, 2024

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atrigila
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@atrigila atrigila commented Aug 9, 2024 •
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Closes #149
Also improves documentation by making even more clear in the usage section the difference between the pipeline samplesheet and the flowcell samplesheet.
Closes #98
Closes #90

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
  • If necessary, also make a PR on the nf-core/demultiplex 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 --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@atrigila atrigila self-assigned this Aug 9, 2024
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github-actions bot commented Aug 9, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 16e6b1a

+| ✅ 191 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-09 22:05:36

@atrigila atrigila marked this pull request as ready for review August 9, 2024 17:24
@atrigila atrigila requested a review from a team as a code owner August 9, 2024 17:24
This was linked to issues Aug 9, 2024
Documentation and file type for SampleSheet.csv #90
Open
Remove confusing samplesheet language #98
Closed
Add samplesheet generation #149
Closed
nschcolnicov
nschcolnicov approved these changes Aug 9, 2024
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Looks good to me!

nschcolnicov
nschcolnicov reviewed Aug 9, 2024
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workflows/demultiplex.nf
@@ -250,6 +252,30 @@ workflow DEMULTIPLEX {
ch_versions = ch_versions.mix(FASTQ_CONTAM_SEQTK_KRAKEN.out.versions)
ch_multiqc_files = ch_multiqc_files.mix( FASTQ_CONTAM_SEQTK_KRAKEN.out.reports.map { meta, log -> return log })
}

// Prepare metamap with fastq info
ch_meta_fastq = ch_raw_fastq.map { meta, fastq_files ->
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I'm curious about this part, not saying to change it, but want to understand why do we need to build the fastq paths for getting the names, shouldn't they be available from the channel?

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The full path of the names from the fastq files point to the work directory instead of the final publish directory. Therefore, we need to obtain the basename and add the publish directory path.

@atrigila atrigila changed the title Add samplesheet generation Add samplesheet generation and improve usage documentation Aug 9, 2024
@apeltzer apeltzer merged commit 8353819 into nf-core:dev Aug 10, 2024
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@nschcolnicov nschcolnicov nschcolnicov approved these changes

@apeltzer apeltzer apeltzer approved these changes

@grst grst Awaiting requested review from grst

@edmundmiller edmundmiller Awaiting requested review from edmundmiller

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