From e286ef6622a97dfbba903e6ac755609490f5cb84 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 23 Jul 2018 13:22:18 +0200
Subject: [PATCH] cutadapt to 1.0
---
cutadapt.wdl | 205 ++++++++++++++++++++++++++-------------------------
1 file changed, 104 insertions(+), 101 deletions(-)
diff --git a/cutadapt.wdl b/cutadapt.wdl
index 3f16d14..66a7106 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -1,108 +1,111 @@
-task cutadapt {
- File read1
- File? read2
- String read1output
- String? read2output
- String? format
- String? preCommand
- Int? cores = 1
- Int? memory = 4
- Array[String]+? adapter
- Array[String]+? front
- Array[String]+? anywhere
- Array[String]+? adapterRead2
- Array[String]+? frontRead2
- Array[String]+? anywhereRead2
- Boolean? interleaved
- String? pairFilter
- Float? errorRate
- Boolean? noIndels
- Int? times
- Int? overlap
- Boolean? matchReadWildcards
- Boolean? noMatchAdapterWildcards
- Boolean? noTrim
- Boolean? maskAdapter
- Int? cut
- String? nextseqTrim
- String? qualityCutoff
- Int? qualityBase
- Int? length
- Boolean? trimN
- String? lengthTag
- String? stripSuffix
- String? prefix
- String? suffix
- Int? minimumLength = 1 # Necessary to prevent creation of empty reads
- Int? maximumLength
- Int? maxN
- Boolean? discardTrimmed
- Boolean? discardUntrimmed
- String? infoFilePath
- String? restFilePath
- String? wildcardFilePath
- String? tooShortOutputPath
- String? tooLongOutputPath
- String? untrimmedOutputPath
- String? tooShortPairedOutputPath
- String? tooLongPairedOutputPath
- String? untrimmedPairedOutputPath
- Boolean? colorspace
- Boolean? doubleEncode
- Boolean? trimPrimer
- Boolean? stripF3
- Boolean? maq
- Boolean? bwa
- Boolean? zeroCap
- Boolean? noZeroCap
- String? reportPath
+version 1.0
+task cutadapt {
+ input {
+ File read1
+ File? read2
+ String read1output
+ String? read2output
+ String? format
+ String? preCommand
+ Int? cores = 1
+ Int? memory = 4
+ Array[String]+? adapter
+ Array[String]+? front
+ Array[String]+? anywhere
+ Array[String]+? adapterRead2
+ Array[String]+? frontRead2
+ Array[String]+? anywhereRead2
+ Boolean? interleaved
+ String? pairFilter
+ Float? errorRate
+ Boolean? noIndels
+ Int? times
+ Int? overlap
+ Boolean? matchReadWildcards
+ Boolean? noMatchAdapterWildcards
+ Boolean? noTrim
+ Boolean? maskAdapter
+ Int? cut
+ String? nextseqTrim
+ String? qualityCutoff
+ Int? qualityBase
+ Int? length
+ Boolean? trimN
+ String? lengthTag
+ String? stripSuffix
+ String? prefix
+ String? suffix
+ Int? minimumLength = 1 # Necessary to prevent creation of empty reads
+ Int? maximumLength
+ Int? maxN
+ Boolean? discardTrimmed
+ Boolean? discardUntrimmed
+ String? infoFilePath
+ String? restFilePath
+ String? wildcardFilePath
+ String? tooShortOutputPath
+ String? tooLongOutputPath
+ String? untrimmedOutputPath
+ String? tooShortPairedOutputPath
+ String? tooLongPairedOutputPath
+ String? untrimmedPairedOutputPath
+ Boolean? colorspace
+ Boolean? doubleEncode
+ Boolean? trimPrimer
+ Boolean? stripF3
+ Boolean? maq
+ Boolean? bwa
+ Boolean? zeroCap
+ Boolean? noZeroCap
+ String? reportPath
+ }
command {
set -e -o pipefail
- ${"mkdir -p $(dirname " + read1output + ")"}
- ${"mkdir -p $(dirname " + read2output + ")"}
- ${"mkdir -p $(dirname " + reportPath + ")"}
- ${preCommand}
+ ~{"mkdir -p $(dirname " + read1output + ")"}
+ ~{"mkdir -p $(dirname " + read2output + ")"}
+ ~{"mkdir -p $(dirname " + reportPath + ")"}
+ ~{preCommand}
cutadapt \
- ${"--cores=" + cores} \
- ${true="-a " false="" defined(adapter)} ${sep=" -a " adapter} \
- ${true="-A " false="" defined(adapterRead2)} ${sep=" -A " adapterRead2} \
- ${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} \
- --output ${read1output} ${"--paired-output " + read2output} \
- ${"--to-short-output " + tooShortOutputPath} ${"--to-short-paired-output " + tooShortPairedOutputPath} \
- ${"--to-long-output " + tooLongOutputPath} ${"--to-long-paired-output " + tooLongPairedOutputPath} \
- ${"--untrimmed-output " + untrimmedOutputPath} ${"--untrimmed-paired-output " + untrimmedPairedOutputPath} \
- ${"--pair-filter " + pairFilter} \
- ${"--error-rate " + errorRate} \
- ${"--times " + times} \
- ${"--overlap " + overlap} \
- ${"--cut " + cut} \
- ${"--nextseq-trim " + nextseqTrim} \
- ${"--quality-cutoff " + qualityCutoff} \
- ${"--quality-base " + qualityBase} \
- ${"--length " + length} \
- ${"--length-tag " + lengthTag} \
- ${"--strip-suffix " + stripSuffix} \
- ${"--prefix " + prefix} \
- ${"--suffix " + suffix} \
- ${"--minimum-length " + minimumLength} \
- ${"--maximum-length " + maximumLength} \
- ${"--max-n " + maxN} \
- ${true="--discard-untrimmed" false="" discardUntrimmed} \
- ${"--info-file " + infoFilePath } \
- ${"--rest-file " + restFilePath } \
- ${"--wildcard-file " + wildcardFilePath} \
- ${true="--match-read-wildcards" false="" matchReadWildcards} ${true="--no-match-adapter-wildcards" false="" noMatchAdapterWildcards} \
- ${true="--no-trim" false="" noTrim} ${true="--mask-adapter" false="" maskAdapter} \
- ${true="--no-indels" false="" noIndels} ${true="--trim-n" false="" trimN} \
- ${true="--interleaved" false="" interleaved} ${true="--discard-trimmed" false="" discardTrimmed } \
- ${true="--colorspace" false="" colorspace} ${true="--double-encode" false="" doubleEncode} \
- ${true="--strip-f3" false="" stripF3} ${true="--maq" false="" maq} ${true="--bwa" false="" bwa} \
- ${true="--zero-cap" false="" zeroCap} ${true="--no-zero-cap" false="" noZeroCap} \
- ${read1} ${read2} ${"> " + reportPath}
+ ~{"--cores=" + cores} \
+ ~{true="-a " false="" defined(adapter)} ~{sep=" -a " adapter} \
+ ~{true="-A " false="" defined(adapterRead2)} ~{sep=" -A " adapterRead2} \
+ ~{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} \
+ --output ~{read1output} ~{"--paired-output " + read2output} \
+ ~{"--to-short-output " + tooShortOutputPath} ~{"--to-short-paired-output " + tooShortPairedOutputPath} \
+ ~{"--to-long-output " + tooLongOutputPath} ~{"--to-long-paired-output " + tooLongPairedOutputPath} \
+ ~{"--untrimmed-output " + untrimmedOutputPath} ~{"--untrimmed-paired-output " + untrimmedPairedOutputPath} \
+ ~{"--pair-filter " + pairFilter} \
+ ~{"--error-rate " + errorRate} \
+ ~{"--times " + times} \
+ ~{"--overlap " + overlap} \
+ ~{"--cut " + cut} \
+ ~{"--nextseq-trim " + nextseqTrim} \
+ ~{"--quality-cutoff " + qualityCutoff} \
+ ~{"--quality-base " + qualityBase} \
+ ~{"--length " + length} \
+ ~{"--length-tag " + lengthTag} \
+ ~{"--strip-suffix " + stripSuffix} \
+ ~{"--prefix " + prefix} \
+ ~{"--suffix " + suffix} \
+ ~{"--minimum-length " + minimumLength} \
+ ~{"--maximum-length " + maximumLength} \
+ ~{"--max-n " + maxN} \
+ ~{true="--discard-untrimmed" false="" discardUntrimmed} \
+ ~{"--info-file " + infoFilePath } \
+ ~{"--rest-file " + restFilePath } \
+ ~{"--wildcard-file " + wildcardFilePath} \
+ ~{true="--match-read-wildcards" false="" matchReadWildcards} ~{true="--no-match-adapter-wildcards" false="" noMatchAdapterWildcards} \
+ ~{true="--no-trim" false="" noTrim} ~{true="--mask-adapter" false="" maskAdapter} \
+ ~{true="--no-indels" false="" noIndels} ~{true="--trim-n" false="" trimN} \
+ ~{true="--interleaved" false="" interleaved} ~{true="--discard-trimmed" false="" discardTrimmed } \
+ ~{true="--colorspace" false="" colorspace} ~{true="--double-encode" false="" doubleEncode} \
+ ~{true="--strip-f3" false="" stripF3} ~{true="--maq" false="" maq} ~{true="--bwa" false="" bwa} \
+ ~{true="--zero-cap" false="" zeroCap} ~{true="--no-zero-cap" false="" noZeroCap} \
+ ~{read1} ~{read2} ~{"> " + reportPath}
}
output{
File report = if defined(reportPath) then select_first([reportPath]) else stdout()
--
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