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Dev - Adding FastQC to the pipeline, with integration into MultiQC #121

Merged
merged 7 commits into from
Jul 5, 2022
Merged

Dev - Adding FastQC to the pipeline, with integration into MultiQC #121

merged 7 commits into from
Jul 5, 2022

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heylf
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@heylf heylf commented Jun 29, 2022

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/scrnaseq 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>).
  • 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).

grst
grst approved these changes Jun 29, 2022
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Looks great! Just two small code questions...

subworkflows/local/fastqc.nf Outdated
Comment on lines 21 to 24
fastqc_zip = Channel.empty()
fastqc_html = Channel.empty()
fastqc_multiqc = Channel.empty()
fastqc_version = Channel.empty()
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Is this necessary?

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no, some are obsolete, which came from old code.

workflows/scrnaseq.nf Outdated
ch_multiqc_fastqc = Channel.empty()
if (!params.skip_fastqc){
FASTQC_CHECK ( ch_fastq )
ch_versions = ch_versions.mix(FASTQC_CHECK.out.fastqc_version.first().ifEmpty(null))
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is .first().ifEmpty(null) required?

We currently don't have it anywhere else for the versions and there should always be a version file emitted...

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I have removed it

@grst grst linked an issue Jun 29, 2022 that may be closed by this pull request
Add FastQC #115
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grst
grst reviewed Jun 29, 2022
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subworkflows/local/fastqc.nf Outdated Show resolved Hide resolved
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github-actions bot commented Jun 29, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 893ae78

+| ✅ 148 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-06-29 19:23:37

@apeltzer
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@nf-core-bot fix linting

@apeltzer apeltzer merged commit abca10c into nf-core:dev Jul 5, 2022
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Add FastQC
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@heylf @apeltzer @grst @nf-core-bot