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Fix No such variable: CUTADAPT error by replacing CUTADAPT.out with C… #187

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merged 3 commits into from
Jul 25, 2024
Merged

Fix No such variable: CUTADAPT error by replacing CUTADAPT.out with C… #187

merged 3 commits into from
Jul 25, 2024

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joannakraw
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Description

In this PR, I've added necessary changes to fix the bug described in Issue #180, connected with No such variable: CUTADAPT bug.

I have resolved this issue locally by making the following changes to workflows/crisprseq_screening.nf:

  • Replaced CUTADAPT.out with CUTADAPT_FIVE_PRIME in line 89.
  • Replaced CUTADAPT.out with CUTADAPT_THREE_PRIME in line 98.

Comments:

  • nf-core lint test passed with 35 test warnings
  • testing with nextflow run . -profile test,docker --outdir <OUTDIR> failed but not due to the changes in workflows/crisprseq_screening.nf, I've attached the nextflow.log file nextflow.log.

I'm not sure how I should edit CHANGELOG or README files, and how to approach the problem of failed tests on different pipeline steps (not the one that I've edited).

I would appreciate your help or guidance @LaurenceKuhl.

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).

Fix No such variable: CUTADAPT error by replacing CUTADAPT.out with C…
70071bf 
…UTADAPT_FIVE_PRIME and CUTADAPT_THREE_PRIME
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @joannakraw,

It looks like this pull-request is has been made against the joannakraw/nf_core_crisprseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the joannakraw/nf_core_crisprseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@joannakraw joannakraw changed the base branch from master to dev July 25, 2024 11:56
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github-actions bot commented Jul 25, 2024 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1da7769

+| ✅ 223 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 2024-07-25 13:57:40

@LaurenceKuhl
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LaurenceKuhl commented Jul 25, 2024 •
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Hi @joannakraw i added something in the readme and the changelog, thanks again for the bug fix :)
Let's see if the tests pass on github

LaurenceKuhl
LaurenceKuhl approved these changes Jul 25, 2024
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Looks good to me thanks again!

@LaurenceKuhl LaurenceKuhl merged commit 71676e6 into nf-core:dev Jul 25, 2024
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@joannakraw
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Thanks for merging @LaurenceKuhl !

@LaurenceKuhl LaurenceKuhl mentioned this pull request Sep 17, 2024
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@joannakraw @LaurenceKuhl