diff --git a/modules/local/plot_homer_annotatepeaks.nf b/modules/local/plot_homer_annotatepeaks.nf index 11ed3daba..3375349a1 100644 --- a/modules/local/plot_homer_annotatepeaks.nf +++ b/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}": diff --git a/tower.yml b/tower.yml new file mode 100644 index 000000000..5b1f5f906 --- /dev/null +++ b/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" diff --git a/workflows/chipseq.nf b/workflows/chipseq.nf index db6699e4d..06b95b37f 100644 --- a/workflows/chipseq.nf +++ b/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]),