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Added unzip feature #116

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Merged
maxulysse merged 6 commits into from
Jan 25, 2024
Merged

Added unzip feature #116

maxulysse merged 6 commits into from
Jan 25, 2024

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@nschcolnicov
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@nschcolnicov nschcolnicov commented Dec 28, 2023 •
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PR checklist

CHANGE SUMMARY

  • Adding the possibility of using gzipped fasta and gtf files as input reference files.
  • I tested running this with the test_full dataset using a gzipped fasta and gtf file and it passed, I also run the test profile using the regular genome files and it passed too.
  • Added the unzip module using the nf-core tooling (nf-core modules install unzip)
  • I ran the nf-core lint command, and then nf-core lint --fix files_unchanged, there is only one issue remaining, which is unrelated to these changes:
image image
  • 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).

@nschcolnicov nschcolnicov mentioned this pull request Dec 28, 2023
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@maxulysse
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maxulysse commented Dec 29, 2023

It feels like you have a couple of template update in your PR, can you check that up?

@nschcolnicov
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nschcolnicov commented Dec 29, 2023

It feels like you have a couple of template update in your PR, can you check that up?

@maxulysse I pulled the latest changes from dev, let me know if there is anything else needed

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github-actions bot commented Jan 24, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 99eb935

+| ✅ 163 tests passed       |+
!| ❗   4 tests had warnings |!
Details

❗ 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 WorkflowRnavar.groovy: Optionally add in-text citation tools to this list.
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-24 21:41:53

@nschcolnicov
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nschcolnicov commented Jan 24, 2024

@maxulysse I see that the only check missing is the "prettier" one, I have run the command prettier --check in the branch and I don't see any issues:
image

Is there a way of knowing what is causing this failed test?

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maxulysse commented Jan 24, 2024

@nf-core-bot fix linting pretty please

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maxulysse commented Jan 24, 2024

@maxulysse I see that the only check missing is the "prettier" one, I have run the command prettier --check in the branch and I don't see any issues:
image

Is there a way of knowing what is causing this failed test?

It should be good now

@maxulysse maxulysse merged commit 9e23fd6 into nf-core:dev Jan 25, 2024
@nschcolnicov nschcolnicov mentioned this pull request Mar 19, 2024
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