Merge pull request #1 from RHReynolds/fix-skip-fastqc

Fix skip fastqc
seqeralabs · Feb 3, 2023 · b3b9239 · b3b9239
2 parents ff12a53 + 0090138
commit b3b9239
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,8 @@ Initial release of nf-core/dragen, created with the [nf-core](https://nf-co.re/)
 
 ### `Fixed`
 
+- Fixed error `Access to 'FASTQC.out' is undefined since the workflow 'FASTQC' has not been invoked before accessing the output attribute` when `-skip_fastqc` enabled by adjusting channel generation
+
 ### `Dependencies`
 
 ### `Deprecated`
diff --git a/workflows/dragen.nf b/workflows/dragen.nf
@@ -84,11 +84,13 @@ workflow DRAGEN {
     //
     // MODULE: Run FastQC
     //
+    ch_multiqc_fastqc = Channel.empty()
     if (!params.skip_fastqc) {
         FASTQC (
             INPUT_CHECK.out.reads
         )
         ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+        ch_multiqc_fastqc = FASTQC.out.zip
     }
 
     if (!params.skip_dragen) {
@@ -155,7 +157,7 @@ workflow DRAGEN {
     ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_fastqc.collect{it[1]}.ifEmpty([]))
 
     MULTIQC (
         ch_multiqc_files.collect()