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Add drugZ as a module #168

Merged
merged 33 commits into from
Aug 1, 2024
Merged

Add drugZ as a module #168

merged 33 commits into from
Aug 1, 2024

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LaurenceKuhl
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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/crisprseq 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).

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github-actions bot commented Jul 6, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3e9c21e

+| ✅ 224 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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 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!

❔ Tests ignored:

  • files_exist - File is ignored: conf/test.config
  • files_exist - File is ignored: conf/test_full.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-01 12:06:44

@LaurenceKuhl
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@nf-core-bot fix linting

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@LaurenceKuhl
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@nf-core-bot fix linting

@LaurenceKuhl
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I'm not sure why pre-commit is leading to an error :/

mashehu
mashehu reviewed Jul 25, 2024
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modules/local/drugz.nf
def foldchange = "${meta.treatment}_vs_${meta.reference}.foldchange".replaceAll(',','_')

"""
drugz.py -i $count_table -o $output -f $foldchange -c $meta.reference -x $meta.treatment $args
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Any way to make this a conda recipe?

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#189 made it into an issue, might try this during the hackathons

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workflows/crisprseq_screening.nf
// Launch module drugZ
if(params.drugz) {
Channel.fromPath(params.drugz)
.splitCsv(header:true, sep:';' )
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Wait, you said comma separated, now you look for a semi-colon?

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I updated the documentation to make it more clear

LaurenceKuhl and others added 4 commits July 25, 2024 08:27
@LaurenceKuhl @mashehu
Update docs/output/screening.md
680b541 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LaurenceKuhl @mashehu
Update docs/usage/screening.md
e6c4478 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LaurenceKuhl @mashehu
Update nextflow_schema.json
d843f86 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LaurenceKuhl
Ran pre commit
5b5042f
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mashehu commented Jul 25, 2024

@nf-core-bot fix linting

@LaurenceKuhl LaurenceKuhl changed the title Pr 122 Add drugZ as a module Aug 1, 2024
mashehu
mashehu approved these changes Aug 1, 2024
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LaurenceKuhl and others added 4 commits August 1, 2024 13:58
@LaurenceKuhl @mashehu
Update bin/BAGEL.py
944d988 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LaurenceKuhl @mashehu
Update .pre-commit-config.yaml
52dd1df 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LaurenceKuhl @mashehu
Update bin/drugz.py
730e7b3 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
@LaurenceKuhl @mashehu
Update bin/BAGEL.py
b0e45e0 
Co-authored-by: Matthias Hörtenhuber <[email protected]>
LaurenceKuhl
LaurenceKuhl commented Aug 1, 2024
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@LaurenceKuhl LaurenceKuhl mentioned this pull request Aug 1, 2024
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@LaurenceKuhl LaurenceKuhl merged commit 5c7d79f into nf-core:dev Aug 1, 2024
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@LaurenceKuhl LaurenceKuhl deleted the pr-122 branch August 1, 2024 14:04
@LaurenceKuhl LaurenceKuhl mentioned this pull request Sep 17, 2024
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@mashehu mashehu mashehu approved these changes

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@LaurenceKuhl @mashehu