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Changed Cutadapt to use nf-core modules #435

Merged
merged 23 commits into from
Oct 25, 2024
Merged

Changed Cutadapt to use nf-core modules #435

merged 23 commits into from
Oct 25, 2024

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svarona
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@svarona svarona commented Jun 18, 2024 •
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Fixes issue #409

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/viralrecon 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).

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github-actions bot commented Jun 18, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e963569

+| ✅ 201 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 base.config: Check the defaults for all processes
  • 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
  • system_exit - System.exit in nanopore.nf: System.exit(1) [line 248]

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-25 14:16:21

@svarona svarona marked this pull request as ready for review June 18, 2024 10:25
svarona added a commit to BU-ISCIII/viralrecon that referenced this pull request Aug 20, 2024
@svarona
Merge pull request #33 from maxulysse/dev
bb917c1 
Fixing merge conflicts on nf-core#435
maxulysse
maxulysse reviewed Oct 7, 2024
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So the issue there is that we no longer have the adapter file in the script and we're trying to pass it within the meta map.
We should only pass files to modules within a channel.
I'd recommend to patch the modules upstream and keep this adapter input

maxulysse
maxulysse requested changes Oct 18, 2024
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We should only pass files to modules within a channel.
I'd recommend to patch the modules upstream and keep this adapter input in cutadapt

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svarona commented Oct 25, 2024

We should only pass files to modules within a channel. I'd recommend to patch the modules upstream and keep this adapter input in cutadapt

Thanks a lot @maxulysse! Just learned about this patch thing thanks to having @Daniel-VM nearby at work! I'm already working on it!!

@maxulysse maxulysse merged commit 402fad8 into nf-core:dev Oct 25, 2024
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@svarona @maxulysse @Joon-Klaps