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Fix gzip error #382

Merged
merged 4 commits into from
Oct 28, 2024
Merged

Fix gzip error #382

merged 4 commits into from
Oct 28, 2024

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esrice
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@esrice esrice commented Oct 11, 2024

Fix #380 --- when giving an un-gzipped whitelist file to the pipeline, both STAR and alevin-fry crash. These two commits fix those two issues, respectively, so that both gzipped and un-gzipped whitelists are allowed.

grst and others added 3 commits August 15, 2024 08:25
@grst
Merge pull request nf-core#356 from nf-core/dev
4171377 
Release v2.7.1
@esrice
Fix nf-core#380
81ba001
@esrice
Fix same error as last commit, but for alevin
017e0d3 
The alevin-fry workflow for this pipeline has the same issue as the STAR
workflow: it assumes the whitelist is gzipped, and crashes if it is not.
This commit fixes that by only trying to unzip the whitelist if it is in
fact gzipped.
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github-actions bot commented Oct 11, 2024 •
edited by nf-core-bot
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 2.14.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@esrice esrice changed the base branch from master to dev October 11, 2024 22:30
grst
grst reviewed Oct 28, 2024
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modules/local/star_align.nf Outdated Show resolved Hide resolved
@esrice
Fix potential filename conflict
9d13a7e 
Call the uncompressed whitelist whitelist.uncompressed.txt instead of
whitelist.txt.
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github-actions bot commented Oct 28, 2024 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9d13a7e

+| ✅ 216 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-28 11:16:48

@grst grst merged commit eaa74dd into nf-core:dev Oct 28, 2024
15 checks passed
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@grst grst grst approved these changes

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Crashes due to trying to unzip file that is not zipped
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@esrice @grst