diff --git a/bioconda.wdl b/bioconda.wdl
index f8c14e7a17eb0d86a0988c8b0288ee0206163cbc..0600ff72d79dc27065fbdb7b6e4db1950e37e710 100644
--- a/bioconda.wdl
+++ b/bioconda.wdl
@@ -20,5 +20,6 @@ task installPrefix {
}
output {
File condaEnvPath=prefix
+ File condaJson=stdout()
}
}
diff --git a/centrifuge.wdl b/centrifuge.wdl
index 55b57739146dbc2255d81d90183ada502f7888b1..9c75f77257b7643c349b243c817499a2477a22cc 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -6,7 +6,7 @@ task download {
String libraryPath
Array[String]? domain
String? executable = "centrifuge-download"
- File? condaEnvironment
+ String? preCommand
String? seqTaxMapPath
String? database = "refseq"
String? assemblyLevel
@@ -22,11 +22,12 @@ task download {
# The bash statement at the beginning is to make sure
# the directory for the SeqTaxMapPath exists.
command {
+ set -e -o pipefail
+ ${preCommand}
${'if [ ! -f ' + seqTaxMapPath +
' ]; then mkdir -p ' + seqTaxMapPath +
'; rm -d ' + seqTaxMapPath +
'; fi' }
- ${"source activate " + condaEnvironment}
${executable} \
-o ${libraryPath} \
${true='-d ' false='' defined(domain)}${sep=',' domain} \
@@ -50,9 +51,10 @@ task download {
task downloadTaxonomy {
String centrifugeTaxonomyDir
String? executable = "centrifuge-download"
- File? condaEnvironment
+ String? preCommand
command {
- ${"source activate " + condaEnvironment}
+ set -e -o pipefail
+ ${preCommand}
${executable} \
-o ${centrifugeTaxonomyDir} \
taxonomy
@@ -69,7 +71,7 @@ task build {
File taxonomyTree
File inputFasta
String centrifugeIndexBase
- File? condaEnvironment
+ String? preCommand
String? centrifugeBuildExecutable = "centrifuge-build"
#Boolean? c = false
Boolean? largeIndex = false
@@ -88,9 +90,10 @@ task build {
Int? kmerCount
command {
+ set -e -o pipefail
+ ${preCommand}
mkdir -p ${centrifugeIndexBase}
rm -d ${centrifugeIndexBase}
- ${"source activate " + condaEnvironment}
${centrifugeBuildExecutable} \
${true='--large-index' false='' largeIndex} \
${true='--noauto' false='' noAuto} \
diff --git a/cutadapt.wdl b/cutadapt.wdl
new file mode 100644
index 0000000000000000000000000000000000000000..f38f2c3d1ed23097b3c9522de656357fcba27dfe
--- /dev/null
+++ b/cutadapt.wdl
@@ -0,0 +1,123 @@
+task cutadapt {
+ File read1
+ File? read2
+ String read1output
+ String? read2output
+ String? format
+ String? preCommand
+ Int? cores = 1
+ String? memory = "4G"
+ 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
+ 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})
+ ${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=" -a " 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()
+ File cutRead1 = read1output
+ File? cutRead2 = read2output
+ File? tooLongOutput=tooLongOutputPath
+ File? tooShortOutput=tooShortOutputPath
+ File? untrimmedOutput=untrimmedOutputPath
+ File? tooLongPairedOutput=tooLongPairedOutputPath
+ File? tooShortPairedOutput=tooShortPairedOutputPath
+ File? untrimmedPairedOutput=untrimmedPairedOutputPath
+ File? infoFile=infoFilePath
+ File? restFile=restFilePath
+ File? wildcardFile=wildcardFilePath
+ }
+ runtime {
+ cpu: select_first([cores])
+ memory: select_first([memory])
+ }
+}
\ No newline at end of file
diff --git a/fastqc.wdl b/fastqc.wdl
new file mode 100644
index 0000000000000000000000000000000000000000..657c7929e2f4afb68cf32def2a158fab1ed98d5d
--- /dev/null
+++ b/fastqc.wdl
@@ -0,0 +1,114 @@
+task fastqc {
+ File seqFile
+ String outdirPath
+ String? preCommand
+ Boolean? casava
+ Boolean? nano
+ Boolean? noFilter
+ Boolean? extract = true
+ Boolean? nogroup
+ Int? minLength
+ String? format
+ Int? threads = 1
+ File? contaminants
+ File? adapters
+ File? limits
+ Int? kmers
+ String? dir
+
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ mkdir -p ${outdirPath}
+ fastqc \
+ ${"--outdir " + outdirPath} \
+ ${true="--casava" false="" casava} \
+ ${true="--nano" false="" nano} \
+ ${true="--nofilter" false="" noFilter} \
+ ${true="--extract" false="" extract} \
+ ${true="--nogroup" false="" nogroup} \
+ ${"--min_length " + minLength } \
+ ${"--format " + format} \
+ ${"--threads " + threads} \
+ ${"--contaminants " + contaminants} \
+ ${"--adapters " + adapters} \
+ ${"--limits " + limits} \
+ ${"--kmers " + kmers} \
+ ${"--dir " + dir} \
+ ${seqFile}
+
+ }
+
+ output {
+ # Chops of the .gz extension if present.
+ String name = sub(seqFile, "\\.gz$","")
+ # This regex chops of the extension and replaces it with _fastqc for the reportdir.
+ # Just as fastqc does it.
+ String reportDir = outdirPath + "/" + sub(basename(name), "\\.[^\\.]*$", "_fastqc")
+ File rawReport = reportDir + "/fastqc_data.txt"
+ File htmlReport = reportDir + "/fastqc_report.html"
+ File summary = reportDir + "/summary.txt"
+ File adapterContent = reportDir + "/Images/adapter_content.png"
+ File duplicationLevels = reportDir + "/Images/duplication_levels.png"
+ File perBaseNContent = reportDir + "/Images/per_base_n_content.png"
+ File perBaseQuality = reportDir + "/Images/per_base_quality.png"
+ File perBaseSequenceContent = reportDir + "/Images/per_base_sequence_content.png"
+ File perSequenceGCContent = reportDir + "/Images/per_sequence_gc_content.png"
+ File perSequenceQuality = reportDir + "/Images/per_sequence_quality.png"
+ File perTileQuality = reportDir + "/Images/per_tile_quality.png"
+ File sequenceLengthDistribution = reportDir + "/Images/sequence_length_distribution.png"
+ }
+
+ runtime {
+ cpu: select_first([threads])
+ }
+}
+
+task extractAdapters {
+ File extractAdaptersFastqcJar
+ File inputFile
+ String outputDir
+ String? adapterOutputFilePath = outputDir + "/adapter.list"
+ String? contamsOutputFilePath = outputDir + "/contaminations.list"
+ Boolean? skipContams
+ File? knownContamFile
+ File? knownAdapterFile
+ Float? adapterCutoff
+ Boolean? outputAsFasta
+ command {
+ set -e
+ mkdir -p ${outputDir}
+ java -jar ${extractAdaptersFastqcJar} \
+ --inputFile ${inputFile} \
+ ${"--adapterOutputFile " + adapterOutputFilePath } \
+ ${"--contamsOutputFile " + contamsOutputFilePath } \
+ ${"--knownContamFile " + knownContamFile} \
+ ${"--knownAdapterFile " + knownAdapterFile} \
+ ${"--adapterCutoff " + adapterCutoff} \
+ ${true="--skipContams" false="" skipContams} \
+ ${true="--outputAsFasta" false="" outputAsFasta}
+ }
+
+ output {
+ File adapterOutputFile = select_first([adapterOutputFilePath])
+ File contamsOutputFile = select_first([contamsOutputFilePath])
+ Array[String] adapterList = read_lines(select_first([adapterOutputFilePath]))
+ Array[String] contamsList = read_lines(select_first([contamsOutputFilePath]))
+ }
+}
+
+task getConfiguration {
+ String? preCommand
+ String? fastqcDirFile = "fastqcDir.txt"
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ echo $(dirname $(readlink -f $(which fastqc))) > ${fastqcDirFile}
+ }
+ output {
+ String fastqcDir = read_string(fastqcDirFile)
+ File adapterList = fastqcDir + "/Configuration/adapter_list.txt"
+ File contaminantList = fastqcDir + "/Configuration/contaminant_list.txt"
+ File limits = fastqcDir + "/Configuration/limits.txt"
+ }
+}
\ No newline at end of file
diff --git a/ncbi.wdl b/ncbi.wdl
index 77fa0c8ce35757f8535f5a1a65f7de9b59ee56bf..f32959ec6ebe01494e2b6faf6ed580c354e6417d 100644
--- a/ncbi.wdl
+++ b/ncbi.wdl
@@ -14,11 +14,11 @@ task genomeDownload {
String? domain = "all"
String? executable = "ncbi-genome-download"
- File? condaEnvironment
+ String? preCommand
command {
set -e -o pipefail
- ${"source activate " + condaEnvironment}
+ ${preCommand}
${executable} \
${"--section " + section} \
${"--format " + format} \