Merge pull request #306 from drpatelh/updates

Add tower.yml file with list of pertinent Reports to display in Tower

modules/local/plot_homer_annotatepeaks.nf

@@ -27,7 +27,7 @@ process PLOT_HOMER_ANNOTATEPEAKS {
         -p $prefix \\
         $args
 
-    find ./ -type f -name "*.txt" -exec cat {} \\; | cat $mqc_header - > ${prefix}.summary_mqc.tsv
+    find ./ -type f -name "*summary.txt" -exec cat {} \\; | cat $mqc_header - > ${prefix}.summary_mqc.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

tower.yml

@@ -0,0 +1,19 @@
+reports:
+  multiqc_report.html:
+    display: "MultiQC HTML report"
+  macs2_peak.plots.pdf:
+    display: "All samples MACS2 peak QC PDF plots"
+  macs2_annotatePeaks.plots.pdf:
+    display: "All samples HOMER annotatePeaks.pl QC PDF plots"
+  "*.consensus_peaks.plots.pdf":
+    display: "Consensus peaks DESeq2 QC PDF plots"
+  "*.consensus_peaks.boolean.intersect.plot.pdf":
+    display: "Consensus peaks UpSetR intersection PDF plots"
+  "*.consensus_peaks.boolean.annotatePeaks.txt":
+    display: "Consensus peaks annotated by HOMER"
+  "*.plotHeatmap.pdf":
+    display: "Per-sample deepTools plotHeatmap PDF plots"
+  "*_peaks.broadPeak":
+    display: "Per-sample MACS2 broadPeak file"
+  "*_peaks.narrowPeak":
+    display: "Per-sample MACS2 narrowPeak file"

workflows/chipseq.nf

@@ -297,7 +297,7 @@ workflow CHIPSEQ {
     ch_versions = ch_versions.mix(MARK_DUPLICATES_PICARD.out.versions)
 
     //
-    // SUBWORKFLOW: Fix getting name sorted BAM here for PE/SE
+    // SUBWORKFLOW: Filter BAM file with BamTools
     //
     FILTER_BAM_BAMTOOLS (
         MARK_DUPLICATES_PICARD.out.bam.join(MARK_DUPLICATES_PICARD.out.bai, by: [0]),