fix multiqc not run

nf-core · Oct 1, 2022 · f8c0cef · f8c0cef
1 parent 3e89a9e
commit f8c0cef
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -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)
 
 /*
@@ -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)