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Avoid publishing uncompressed VCF-file from HMTNOTE_ANNOTATE #368

Merged
merged 5 commits into from
Jul 6, 2023
Merged

Avoid publishing uncompressed VCF-file from HMTNOTE_ANNOTATE #368

merged 5 commits into from
Jul 6, 2023

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asp8200
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@asp8200 asp8200 commented Jun 29, 2023 •
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Related to issue #243

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/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 Jun 29, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e8599cd

+| ✅ 154 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-06 12:09:02

@asp8200 asp8200 requested review from jemten and ramprasadn July 6, 2023 11:56
@asp8200 asp8200 changed the title Compress output Avoid publishing uncompressed VCF-file from HMTNOTE_ANNOTATE Jul 6, 2023
@asp8200 asp8200 marked this pull request as ready for review July 6, 2023 12:43
jemten
jemten approved these changes Jul 6, 2023
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👍

@asp8200 asp8200 merged commit 4d37b19 into nf-core:dev Jul 6, 2023
@asp8200 asp8200 deleted the compress_output branch July 6, 2023 16:47
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@jemten jemten jemten approved these changes

@ramprasadn ramprasadn Awaiting requested review from ramprasadn

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