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Get rid of lib to merge tools v2.13.1 #357

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merged 15 commits into from Apr 2, 2024
Merged

Get rid of lib to merge tools v2.13.1 #357

merged 15 commits into from Apr 2, 2024

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JoseEspinosa
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Closes #356

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

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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-atacseq 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-atacseq 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!

@JoseEspinosa JoseEspinosa changed the base branch from master to dev March 20, 2024 12:34
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github-actions bot commented Mar 20, 2024 •
edited

nf-core lint overall result: Failed ❌

Posted for pipeline commit eb1285a

+| ✅ 175 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!
-| ❌   6 tests failed       |-

❌ Test failures:

❗ Test warnings:

  • 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!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-02 09:08:05

@JoseEspinosa JoseEspinosa marked this pull request as ready for review March 20, 2024 14:26
bjlang
bjlang requested changes Mar 22, 2024
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result/pipeline_info/params_2024-03-19_16-59-36.json Outdated Show resolved Hide resolved
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lib/WorkflowAtacseq.groovy Show resolved Hide resolved
subworkflows/local/utils_nfcore_atacseq_pipeline/main.nf Outdated Show resolved Hide resolved
subworkflows/local/utils_nfcore_atacseq_pipeline/main.nf
return reference_text
}

def methodsDescriptionText(mqc_methods_yaml) {
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Where is this function used?

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This is added by the template to make possible to dump the reference e.g. here.

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And yes I think we can leave this to the template merge

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bjlang
bjlang approved these changes Apr 2, 2024
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LGTM

@JoseEspinosa JoseEspinosa merged commit 36227a2 into nf-core:dev Apr 2, 2024
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@bjlang bjlang bjlang approved these changes

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Get template v2.13.1 (get rid of lib)
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@JoseEspinosa @bjlang