From 62b74c14b556b3bac9efb00c2c42d6c05031b710 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 11 Mar 2020 16:37:33 +0100
Subject: [PATCH] make statsPrefix optional for umitools dedup
---
umi-tools.wdl | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/umi-tools.wdl b/umi-tools.wdl
index e684ef5..35d5429 100644
--- a/umi-tools.wdl
+++ b/umi-tools.wdl
@@ -71,10 +71,10 @@ task Dedup {
File inputBam
File inputBamIndex
String outputBamPath
- String statsPrefix = "stats"
+ String? statsPrefix
Boolean paired = true
- String memory = "20G"
+ String memory = "5G"
# Use a multi-package-container which includes umi_tools (0.5.5) and samtools (1.9)
String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:6089936aca6219b5bb5f54210ac5eb456c7503f2-0"
@@ -88,7 +88,7 @@ task Dedup {
umi_tools dedup \
--stdin ~{inputBam} \
--stdout ~{outputBamPath} \
- --output-stats ~{statsPrefix} \
+ ~{"--output-stats " + statsPrefix} \
~{true="--paired" false="" paired}
samtools index ~{outputBamPath} ~{outputBamIndex}
}
@@ -96,9 +96,9 @@ task Dedup {
output {
File deduppedBam = outputBamPath
File deduppedBamIndex = outputBamIndex
- File editDistance = statsPrefix + "_edit_distance.tsv"
- File umiStats = statsPrefix + "_per_umi.tsv"
- File positionStats = statsPrefix + "_per_umi_per_position.tsv"
+ File? editDistance = statsPrefix + "_edit_distance.tsv"
+ File? umiStats = statsPrefix + "_per_umi.tsv"
+ File? positionStats = statsPrefix + "_per_umi_per_position.tsv"
}
runtime {
--
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