Add deseq and fix homer annotate peaks in multiqc

Author: JoseEspinosa

modules/local/multiqc.nf

@@ -44,6 +44,9 @@ process MULTIQC {
 
     path ('featurecounts/*')
 
+    path ('deseq2/*')
+    path ('deseq2/*')
+
     output:
     path "*multiqc_report.html", emit: report
     path "*_data"              , emit: data

workflows/chipseq.nf

@@ -582,6 +582,8 @@ workflow CHIPSEQ {
                 ch_deseq2_pca_header,
                 ch_deseq2_clustering_header
             )
+            ch_deseq2_pca_multiqc        = DESEQ2_QC.out.pca_multiqc
+            ch_deseq2_clustering_multiqc = DESEQ2_QC.out.dists_multiqc
         }
     }
 
@@ -654,9 +656,10 @@ workflow CHIPSEQ {
 
             ch_custompeaks_frip_multiqc.collect{it[1]}.ifEmpty([]),
             ch_custompeaks_count_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_plothomerannotatepeaks_multiqc.collect{it[1]}.ifEmpty([]),
-            ch_subreadfeaturecounts_multiqc.collect{it[1]}.ifEmpty([])//,
-            // path ('macs/consensus/*') from ch_macs_consensus_deseq_mqc.collect().ifEmpty([])
+            ch_plothomerannotatepeaks_multiqc.collect().ifEmpty([]),
+            ch_subreadfeaturecounts_multiqc.collect{it[1]}.ifEmpty([]),
+            ch_deseq2_pca_multiqc.collect().ifEmpty([]),
+            ch_deseq2_clustering_multiqc.collect().ifEmpty([])
         )
         multiqc_report       = MULTIQC.out.report.toList()
     }