fix multiqc in template

nf-core · Oct 1, 2022 · 7164f2d · 7164f2d
1 parent 0af65f5
commit 7164f2d
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Showing 2 changed files with 9 additions and 8 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -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 in pipeline
 
 ### Linting
 

diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -23,10 +23,10 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-ch_multiqc_config          = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config   = params.multiqc_config ? file( params.multiqc_config, checkIfExists: true ) : Channel.empty()
-ch_multiqc_logo            = params.multiqc_logo   ? file( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
-ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
+ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
+ch_multiqc_custom_methods_description = params.multiqc_methods_description ? Channel.fromPath(params.multiqc_methods_description, checkIfExists: true) : Channel.fromPath("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -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()
@@ -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(),
+        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)