Skip to content
Snippets Groups Projects
Commit e286ef66 authored by Ruben Vorderman's avatar Ruben Vorderman
Browse files

cutadapt to 1.0

parent c9c2fc44
No related branches found
No related tags found
1 merge request!34Move all files to version 1.0
Hide whitespace changes
Inline Side-by-side
Showing
with 104 additions and 101 deletions
cutadapt.wdl
+ 104
− 101
View file @ e286ef66
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()
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment