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Replaced UNZIP with GUNZIP #136

Merged
merged 2 commits into from
Mar 19, 2024
Merged

Replaced UNZIP with GUNZIP #136

merged 2 commits into from
Mar 19, 2024

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nschcolnicov
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@nschcolnicov nschcolnicov commented Mar 19, 2024 •
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This PR addresses this issue: #135

My original PR for adding the UNZIP feature (#116) wasn't working on AWS. I was building the path to the unzipped file using the map operator on the outputted file because the nf-core module was outputting folder that contained the unzipped file, and the other modules required the full path of the actual unzipped file.
To avoid this, I switched to using the GUNZIP module, which I saw is the one being used in the nf-core/rnaseq pipeline, and it is now working for both running it on the cluster and on aws.

To run the test I just downloaded the fasta and gtf files from the test.profile, gzipped them, and ran the following command:
nextflow run nschcolnicov/rnavar -r fix_unzip -latest -profile cluster,bi,test --fasta ../ref/genome.fasta.gz --gtf ../ref/genome.gtf.gz --outdir .

This worked OK:
image

And for testing the pipeline in AWS, I ran almost the same command:
nextflow run ../../main.nf -profile aws,bi,test --fasta ../ref/genome.fasta.gz --gtf ../ref/genome.gtf.gz --outdir .

Also worked OK:

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/rnavar 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 Mar 19, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 4438535

+| ✅ 177 tests passed       |+
!| ❗   4 tests had warnings |!
-| ❌  10 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowRnavar.groovy
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 WorkflowRnavar.groovy: Optionally add in-text citation tools to this list.

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-19 20:45:35

maxulysse
maxulysse reviewed Mar 19, 2024
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@nf-core-bot fix linting pretty please 🥺

@maxulysse
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Looking good, I'll merge template separately, so not to worry too much about that

@maxulysse maxulysse merged commit 45c2b2a into nf-core:dev Mar 19, 2024
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@maxulysse maxulysse maxulysse approved these changes

@nf-core-bot nf-core-bot Awaiting requested review from nf-core-bot

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@nschcolnicov @maxulysse