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Use standard process to auto-detect whether biotype entry exists in GTF file #607

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merged 5 commits into from
Apr 24, 2021
Merged

Use standard process to auto-detect whether biotype entry exists in GTF file #607

merged 5 commits into from
Apr 24, 2021

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drpatelh
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@drpatelh drpatelh commented Apr 23, 2021 •
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Bypass nextflow-io/nextflow#2060 by using a standard process with awk rather than a native Groovy process.

Tested my branch via Tower on AWS and the pipeline is now running as expected with -profile test.

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@drpatelh drpatelh changed the title Attributes Use standard process to auto-detect whether biotype entry exists in GTF file Apr 23, 2021
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github-actions bot commented Apr 23, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 96103c9

+| ✅ 105 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 1.13.3
  • Run at 2021-04-23 21:33:23

ewels
ewels approved these changes Apr 24, 2021
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changelog..? 🤔

modules/local/attribute_in_gtf.nf Show resolved Hide resolved
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Thanks muchly @ewels ! This is a fix for a fix which has already been added to the CHANGELOG.

@drpatelh drpatelh merged commit 0937395 into nf-core:dev Apr 24, 2021
@drpatelh drpatelh mentioned this pull request Apr 26, 2021
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@ewels ewels ewels approved these changes

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