From d993500b08a8cf26fa5c516392d47b99425107be Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 9 May 2019 08:58:29 +0200
Subject: [PATCH] allow for single adapter and contaminations input in cutadapt
---
cutadapt.wdl | 24 +++++++++++++++++++-----
1 file changed, 19 insertions(+), 5 deletions(-)
diff --git a/cutadapt.wdl b/cutadapt.wdl
index 32ca269..f5f98b1 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -13,6 +13,10 @@ task Cutadapt {
Array[String]+? adapterRead2
Array[String]+? frontRead2
Array[String]+? anywhereRead2
+ # FIXME: default should be set at the subworkflow level, not here. Needs to wait for cromwell fix.
+ Array[String]+? adapterBoth = ["AGATCGGAAGAG"]
+ # contaminations = anywhereBoth
+ Array[String]+? contaminations
Boolean? interleaved
String? pairFilter
Float? errorRate
@@ -33,7 +37,7 @@ task Cutadapt {
String? stripSuffix
String? prefix
String? suffix
- Int? minimumLength = 1 # Necessary to prevent creation of empty reads
+ Int? minimumLength = 2 # Necessary to prevent creation of empty reads or 1 base reads.
Int? maximumLength
Int? maxN
Boolean? discardTrimmed
@@ -66,6 +70,16 @@ task Cutadapt {
then "mkdir -p $(dirname " + read2output + ")"
else ""
+ # Some WDL magic here to set both adapters with one setting.
+ # If then else's are needed to keep the variable optional and undefined
+ Array[String]+? adapterForward = if (defined(adapter) || defined(adapterBoth)) then select_first([adapter, adapterBoth]) else adapter
+ # Assume adapterRead2 will not be set when read2 is not set.
+ Array[String]+? adapterReverse = if defined(read2) then select_first([adapterRead2, adapterBoth]) else adapterRead2
+
+ # Same for contaminations
+ Array[String]+? anywhereForward = if (defined(anywhere) || defined(contaminations)) then select_first([anywhere, contaminations]) else anywhere
+ Array[String]+? anywhereReverse = if (defined(anywhereRead2) || defined(contaminations)) then select_first([anywhereRead2, contaminations]) else anywhereRead2
+
command {
set -e
~{"mkdir -p $(dirname " + read1output + ")"}
@@ -73,12 +87,12 @@ task Cutadapt {
~{"mkdir -p $(dirname " + reportPath + ")"}
cutadapt \
~{"--cores=" + cores} \
- ~{true="-a" false="" defined(adapter)} ~{sep=" -a " adapter} \
- ~{true="-A" false="" defined(adapterRead2)} ~{sep=" -A " adapterRead2} \
+ ~{true="-a" false="" defined(adapterForward)} ~{sep=" -a " adapterForward} \
+ ~{true="-A" false="" defined(adapterReverse)} ~{sep=" -A " adapterReverse} \
~{true="-g" false="" defined(front)} ~{sep=" -g " front} \
~{true="-G" false="" defined(frontRead2)} ~{sep=" -G " frontRead2} \
- ~{true="-b" false="" defined(anywhere)} ~{sep=" -b " anywhere} \
- ~{true="-B" false="" defined(anywhereRead2)} ~{sep=" -B " anywhereRead2} \
+ ~{true="-b" false="" defined(anywhereForward)} ~{sep=" -b " anywhereForward} \
+ ~{true="-B" false="" defined(anywhereReverse)} ~{sep=" -B " anywhereReverse} \
--output ~{read1output} ~{"--paired-output " + read2output} \
~{"--to-short-output " + tooShortOutputPath} \
~{"--to-short-paired-output " + tooShortPairedOutputPath} \
--
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