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correct merging error #437

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wants to merge 7 commits into from
Closed

correct merging error #437

wants to merge 7 commits into from

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ftabaro
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@ftabaro ftabaro commented Nov 28, 2024

This PR just adds back the line to fix GFFREAD that got lost during merge of PR #435.

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github-actions bot commented Nov 28, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 671de70

+| ✅ 235 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   6 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!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • 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 3.0.2
  • Run at 2024-11-28 12:56:56

JoseEspinosa
JoseEspinosa requested changes Dec 23, 2024
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Thanks! Please fix the issues commented on the PR

modules/local/multiqc.nf
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/multiqc:1.23--pyhdfd78af_0' :
'biocontainers/multiqc:1.23--pyhdfd78af_0' }"
conda "bioconda::multiqc=1.25.1"
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These changes have already been included on #436, if would be great if you could do a clean PR only with the fix

CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [[PR #434](https://github.com/nf-core/chipseq/pull/434)] - Prevent pipeline fails from erroneous param validation when igenomes is used.
- [[#432](https://github.com/nf-core/chipseq/issues/432)] - Fix `GFFREAD` call to have the two expected input channels.
- [[#428](https://github.com/nf-core/chipseq/issues/428)] - Bump MultiQC version to 1.25.1
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Please update changelog with the corresponding message, this refers to the previous PR #436

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I will close this PR as there were some leaks from your previous PR and this has already been fixed in #444

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@ftabaro @JoseEspinosa