From 8fcd2e2598fbc340abdda2b3a3d56dae04cb6bdf Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 25 Feb 2022 12:41:51 +0100
Subject: [PATCH] add linx visualisation output
---
hmftools.wdl | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/hmftools.wdl b/hmftools.wdl
index c852b52..c1a824c 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -632,7 +632,7 @@ task LinxVisualisations {
String memory = "9G"
String javaXmx = "8G"
- Int timeMinutes = 10
+ Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/hmftools-linx:1.18--hdfd78af_0"
}
@@ -647,12 +647,13 @@ task LinxVisualisations {
-circos /usr/local/bin/circos \
-vis_file_dir ~{sub(linxOutput[0], basename(linxOutput[0]), "")} \
-data_out ~{outputDir}/circos \
- -plot_out ~{outputDir}/plot \
+ -plot_out ~{outputDir}/plots \
~{if plotReportable then "-plot_reportable" else ""}
}
output {
-
+ Array[File] circos = glob("~{outputDir}/circos/*")
+ Array[File] plots = glob("~{outputDir}/plots/*"
}
runtime {
--
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