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Add tower.yml file with list of pertinent Reports to display in Tower #306

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Merged
merged 3 commits into from
Sep 16, 2022
Merged

Add tower.yml file with list of pertinent Reports to display in Tower #306

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ce0ed8d
Remove redundanct comment
drpatelh Sep 16, 2022
bcc9702
Change find command to be more specific
drpatelh Sep 16, 2022
255992d
Add tower.yml to render Reports for main files on Tower
drpatelh Sep 16, 2022
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2 changes: 1 addition & 1 deletion modules/local/plot_homer_annotatepeaks.nf
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Expand Up @@ -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
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@drpatelh drpatelh Sep 16, 2022 •
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Fixed bug noticed whilst testing on Azure where MultiQC sections were being rendered in the wrong order in the report. Still need to test but I suspect it is happening due to this line. Basically the script is pickup up all files ending in .txt because they are copied into the work directory and hence appending the contents to summary_mqc.tsv which then doesn't render in MultiQC properly.

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@robsyme robsyme Sep 16, 2022

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Great catch. I can see the *peaks.annotatePeaks.txt files in the working directory which would have been picked up in error!


cat <<-END_VERSIONS > versions.yml
"${task.process}":
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19 changes: 19 additions & 0 deletions tower.yml
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@@ -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"
2 changes: 1 addition & 1 deletion workflows/chipseq.nf
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Expand Up @@ -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]),
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