Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

correct merging error #437

Open
wants to merge 7 commits into
base: dev
Choose a base branch
from
Open

correct merging error #437

wants to merge 7 commits into from

Conversation

ftabaro
Copy link

@ftabaro ftabaro commented Nov 28, 2024

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

@github-actions GitHub Actions
Copy link

github-actions bot commented Nov 28, 2024 •
edited
Loading

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
View reviewed changes
Copy link
Member

@JoseEspinosa JoseEspinosa left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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"
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Please update changelog with the corresponding message, this refers to the previous PR #436

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@JoseEspinosa JoseEspinosa JoseEspinosa requested changes

Requested changes must be addressed to merge this pull request.

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@ftabaro @JoseEspinosa