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unselected RNA-seq based workflow #334

Merged
merged 49 commits into from
Jul 17, 2024
Merged

unselected RNA-seq based workflow #334

merged 49 commits into from
Jul 17, 2024

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mapo9
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@mapo9 mapo9 commented May 16, 2024

This PR allows to run airrflow from unselected RNA-seq fastq files. This is done by using the TRUST4 tool.

  • bulk: airrflow runs trust4 and uses TRUST_airr.tsv in the immcantation framework
  • single-cell: airrflow runs trust4 and uses TRUST_barcodes_airr.tsv in the immcantation framework

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/airrflow branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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).

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mapo9 commented May 16, 2024

see also this PR 316 which this PR is based on.

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github-actions bot commented May 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cfa4f73

+| ✅ 274 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-17 19:37:23

@mapo9 mapo9 requested a review from ggabernet May 16, 2024 11:18
@mapo9 mapo9 marked this pull request as draft May 17, 2024 14:09
@mapo9 mapo9 marked this pull request as ready for review May 21, 2024 09:21
ggabernet
ggabernet reviewed May 21, 2024
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@mapo9 I've just started checking at the code and testing it. I already have some comments but still need to check it and test it further. Also I just merged the test data into the nf-core repo so the tests can run

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ggabernet
ggabernet reviewed May 29, 2024
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mapo9 commented Jun 7, 2024 •
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Hi
I incorporated the changes we discussed. Among others, I updated the nf-core/trust4 module which now fits our use-case and switched to the nf-core module in airrflow as well.

ggabernet
ggabernet approved these changes Jul 17, 2024
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I think I fixed the issue that made tests fail, let's see if they pass now

subworkflows/local/fastq_input_check.nf
array = [ meta, [ file(col.filename_R1), file(col.filename_R2) ] ]
if (params.index_file) {
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@mapo9 this part was the one causing the other processes to fail, I fixed it now

@ggabernet ggabernet merged commit 91777ac into nf-core:dev Jul 17, 2024
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