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Published 20 hours ago • verified publisher icon nf-core

Update module sratools prefetch

Open suhrig opened this issue 1 year ago • 3 comments

This PR fixes #285. Downloads using sratools often resulted in corrupt files, because the tool to check the file integrity, vdb-validate is not always reliable. This PR updates the module sratools/prefetch, which includes a fix which performs a manual MD5 sum check in cases where vdb-validate is unreliable.

PR checklist

  • [X] This comment contains a description of changes (with reason).
  • [ ] If you've fixed a bug or added code that should be tested, add tests!
  • [X] Make sure your code lints (nf-core lint).
  • [X] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • [X] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • [X] CHANGELOG.md is updated.

suhrig avatar Apr 08 '24 09:04 suhrig

This PR is against the master branch :x:

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @suhrig,

It looks like this pull-request is has been made against the suhrig/fetchngs master branch. The master branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to master are only allowed if they come from the suhrig/fetchngs dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions[bot] avatar Apr 08 '24 09:04 github-actions[bot]

nf-core lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 3056a3a

+| ✅ 155 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   4 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml

:grey_question: Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-08 12:52:28

github-actions[bot] avatar Apr 08 '24 09:04 github-actions[bot]

Hi @maxulysse, can I help you with the additional checks? All I can say is I have run this several times now without any issues. Regards, Sebastian

suhrig avatar Apr 27 '24 03:04 suhrig