From 799811db76b369b057aa54555e08c3025c6905a0 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Tue, 8 Mar 2022 10:38:40 +0100
Subject: [PATCH] fix cupGenerateReport
---
hmftools.wdl | 22 +++++++++++++---------
1 file changed, 13 insertions(+), 9 deletions(-)
diff --git a/hmftools.wdl b/hmftools.wdl
index d9dea38..2e294ec 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -195,15 +195,19 @@ task CupGenerateReport {
~{sampleName} \
workdir/
mv -t ~{outputDir} \
- ./workdir/~{sampleName}.cup.report.summry.png \
- ./workdir/~{sampleName}.cup.report.features.png \
- ./workdir/~{sampleName}_cup.report.pdf
+ ./workdir/~{sampleName}.cup.report.summary.png \
+ ./workdir/~{sampleName}_cup_report.pdf
+ if [ -f ./workdir/~{sampleName}.cup.report.features.png ]
+ then
+ mv -t ~{outputDir} \
+ ./workdir/~{sampleName}.cup.report.features.png
+ fi
}
output {
- File summaryPng = "~{outputDir}/~{sampleName}.cup.report.summry.png"
- File featuresPng = "~{outputDir}/~{sampleName}.cup.report.features.png"
- File reportPdf = "~{outputDir}/~{sampleName}_cup.report.pdf"
+ File summaryPng = "~{outputDir}/~{sampleName}.cup.report.summary.png"
+ File? featuresPng = "~{outputDir}/~{sampleName}.cup.report.features.png"
+ File reportPdf = "~{outputDir}/~{sampleName}_cup_report.pdf"
}
runtime {
@@ -765,7 +769,7 @@ task Orange {
Array[File]+ linxPlots
File cuppaResultCsv
File cuppaSummaryPlot
- File cuppaFeaturePlot
+ File? cuppaFeaturePlot
File chordPredictionTxt
File peachGenotypeTsv
File protectEvidenceTsv
@@ -812,7 +816,7 @@ task Orange {
-linx_plot_directory ~{sub(linxPlots[0], basename(linxPlots[0]), "")} \
-cuppa_result_csv ~{cuppaResultCsv} \
-cuppa_summary_plot ~{cuppaSummaryPlot} \
- -cuppa_feature_plot ~{cuppaFeaturePlot} \
+ ~{"-cuppa_feature_plot " + cuppaFeaturePlot} \
-chord_prediction_txt ~{chordPredictionTxt} \
-peach_genotype_tsv ~{peachGenotypeTsv} \
-protect_evidence_tsv ~{protectEvidenceTsv} \
@@ -861,7 +865,7 @@ task Orange {
linxPlots: {description: "The plots generated by linx.", category: "required"}
cuppaResultCsv: {description: "The cuppa results csv.", category: "required"}
cuppaSummaryPlot: {description: "The cuppa summary plot.", category: "required"}
- cuppaFeaturePlot: {description: "The cuppa feature plot.", category: "required"}
+ cuppaFeaturePlot: {description: "The cuppa feature plot.", category: "common"}
chordPredictionTxt: {description: "Chord prediction results.", category: "required"}
peachGenotypeTsv: {description: "Genotype tsv produced by peach.", category: "required"}
protectEvidenceTsv: {description: "Evidence tsv produced by protect.", category: "required"}
--
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