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

Fix multiqc in template #1855

Merged
merged 3 commits into from
Oct 1, 2022
Merged

Fix multiqc in template #1855

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
3e89a9e
fix template
ggabernet Oct 1, 2022
f8c0cef
fix multiqc not run
ggabernet Oct 1, 2022
cd5a32b
update changelog
ggabernet Oct 1, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
- Update MultiQC module, update supplying MultiQC default and custom config and logo files to module
- Add a 'recommend' methods description text to MultiQC to help pipeline users report pipeline usage in publications ([#1749](https://github.com/nf-core/tools/pull/1749))
- Fix template spacing modified by JINJA ([#1830](https://github.com/nf-core/tools/pull/1830))
- Fix MultiQC execution on template [#1855](https://github.com/nf-core/tools/pull/1855)

### Linting

Expand Down
14 changes: 7 additions & 7 deletions nf_core/pipeline-template/workflows/pipeline.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,9 +23,9 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

ch_multiqc_config = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
ch_multiqc_custom_config = params.multiqc_config ? file( params.multiqc_config, checkIfExists: true ) : Channel.empty()
ch_multiqc_logo = params.multiqc_logo ? file( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)

/*
Expand Down Expand Up @@ -91,7 +91,7 @@ workflow {{ short_name|upper }} {
workflow_summary = Workflow{{ short_name[0]|upper }}{{ short_name[1:] }}.paramsSummaryMultiqc(workflow, summary_params)
ch_workflow_summary = Channel.value(workflow_summary)

methods_description = WorkflowTestpipeline.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description)
methods_description = Workflow{{ short_name[0]|upper }}{{ short_name[1:] }}.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description)
ch_methods_description = Channel.value(methods_description)

ch_multiqc_files = Channel.empty()
Expand All @@ -102,9 +102,9 @@ workflow {{ short_name|upper }} {

MULTIQC (
ch_multiqc_files.collect(),
ch_multiqc_config,
ch_multiqc_custom_config,
ch_multiqc_logo
ch_multiqc_config.collect().ifEmpty([]),
ch_multiqc_custom_config.collect().ifEmpty([]),
ch_multiqc_logo.collect().ifEmpty([])
)
multiqc_report = MULTIQC.out.report.toList()
ch_versions = ch_versions.mix(MULTIQC.out.versions)
Expand Down