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Rename outputs #516

Merged
merged 7 commits into from
Feb 16, 2024
Merged

Rename outputs #516

merged 7 commits into from
Feb 16, 2024

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ramprasadn
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PR checklist

This PR standardizes outputs file names so they are more readable and logical.

  • 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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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 Feb 14, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3099751

+| ✅ 182 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

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

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-16 12:57:42

@ramprasadn ramprasadn marked this pull request as ready for review February 16, 2024 08:08
@ramprasadn ramprasadn linked an issue Feb 16, 2024 that may be closed by this pull request
Standardize naming of outfiles #492
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jemten
jemten reviewed Feb 16, 2024
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@jemten jemten left a comment •
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Nice to start harmonizing the file names. It For us it would be good to know roughly what the file contains when all the output files are gathered in one folder. For examples the output from the mitochondria deletion process is just <sample_id>.txt.

raredisease/docs/output.md

Line 459 in 27f0aae

- `<sample_id>.txt`: file containing deletions.

Would be good to name it something like <sample_id>_mitochondria_deletions.txt or the old <sample_id>_mitodel.txt Could even use the .tsv ending if we want since I think it's a tab separated file if remember correctly.

docs/output.md Outdated
Comment on lines 269 to 270
- `<case_id>_nomito.vcf.gz`: normalized vcf file containing no MT variants.
- `<case_id>_nomito.vcf.gz.tbi`: index of the vcf file containing no MT variants.
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I think that it would be better to have a filename that describes what the file contains rather than what it doesn't contain. Would be great to link it to what we call the annotated files so that the connection is clear. This would then be <case_id>_snv.vcf.gz

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sounds good 👍🏻

jemten
jemten approved these changes Feb 16, 2024
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Looks good!

@ramprasadn ramprasadn merged commit 6e04808 into nf-core:dev Feb 16, 2024
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@jemten jemten deleted the rename_outputs branch February 20, 2024 08:48
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@jemten jemten jemten approved these changes

@Lucpen Lucpen Awaiting requested review from Lucpen

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Standardize naming of outfiles
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@ramprasadn @jemten