add files to multiqc

nf-core · Oct 17, 2024 · 898306e · 898306e
1 parent 1d63040
commit 898306e
Showing 1 changed file with 10 additions and 0 deletions.
diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf
@@ -199,6 +199,16 @@ workflow RNAFUSION {
             sort: true
         )
     )
+    ch_multiqc_files                      = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(TRIM_WORKFLOW.out.ch_fastp_html.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(TRIM_WORKFLOW.out.ch_fastp_json.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(TRIM_WORKFLOW.out.ch_fastqc_trimmed.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(STARFUSION_WORKFLOW.out.star_stats.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(STARFUSION_WORKFLOW.out.star_gene_count.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(QC_WORKFLOW.out.rnaseq_metrics.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(QC_WORKFLOW.out.duplicate_metrics.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(QC_WORKFLOW.out.insertsize_metrics.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(FUSIONINSPECTOR_WORKFLOW.out.ch_arriba_visualisation.collect{it[1]}.ifEmpty([]))
 
     MULTIQC (
         ch_multiqc_files.collect(),