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Fix bug when --bowtie_indices is provided via the CLI #165

Merged
merged 2 commits into from
Jun 27, 2022
Merged

Fix bug when --bowtie_indices is provided via the CLI #165

merged 2 commits into from
Jun 27, 2022

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JoseEspinosa
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Fixes #159
The problem was that not all the index files were staged in the work dir, see #159 for more background.

PR checklist

  • This comment contains a description of changes (with reason).
  • CHANGELOG.md is updated.

@JoseEspinosa JoseEspinosa changed the base branch from master to dev June 27, 2022 14:47
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This PR is against the master branch ❌

  • 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 @JoseEspinosa,

It looks like this pull-request is has been made against the JoseEspinosa/nf-core-smrnaseq 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 JoseEspinosa/nf-core-smrnaseq 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!

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github-actions bot commented Jun 27, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 31103e0

+| ✅ 145 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-06-27 14:53:18

@apeltzer apeltzer added this to the Release 2.1.0 milestone Jun 27, 2022
@JoseEspinosa JoseEspinosa marked this pull request as ready for review June 27, 2022 15:38
@JoseEspinosa JoseEspinosa merged commit 52776e5 into nf-core:dev Jun 27, 2022
@JoseEspinosa JoseEspinosa mentioned this pull request Jun 27, 2022
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@apeltzer apeltzer apeltzer approved these changes

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--bowtie_indices fails
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@JoseEspinosa @apeltzer