diff --git a/LICENSE b/LICENSE
index 6e2dff36af8a00f40e4ad9e07e7c282111f72da0..ab753ec28bc50c6c26c03748188fcc7013efb274 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
MIT License
-Copyright (c) 2018 Peter van 't Hof
+Copyright (c) Sequencing Analysis Support Core - Leiden University Medical Center
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
diff --git a/bwa.wdl b/bwa.wdl
index 0a8b37fa8ad3fec1d7d3400f6e9b4b5d342dba0a..ffa42313dad13f0c13df6f9c77f938567c0027a0 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -3,6 +3,7 @@ task BwaMem {
File inputR1
File? inputR2
String referenceFasta
+ Array[File] indexFiles # These indexFiles need to be added, otherwise cromwell will not find them.
String outputPath
String? readgroup
@@ -26,3 +27,39 @@ task BwaMem {
memory: if defined(memory) then memory else 8
}
}
+
+task index {
+ File fasta
+ String? preCommand
+ String? constructionAlgorithm
+ Int? blockSize
+ String? outputDir
+ String fastaFilename = basename(fasta)
+
+ command {
+ set -e -o pipefail
+ ${"mkdir -p " + outputDir}
+ ${preCommand}
+ if [[ ! '${outputDir}' = '' ]]
+ then
+ ln -sf ${fasta} ${outputDir + "/"}${fastaFilename}
+ fi
+ bwa index \
+ ${"-a " + constructionAlgorithm} \
+ ${"-b" + blockSize} \
+ ${outputDir + "/"}${fastaFilename}
+ }
+
+ output {
+ File indexBase = if (defined(outputDir)) then select_first([outputDir]) + "/" + fastaFilename else fastaFilename
+ File indexedFasta = indexBase
+ Array[File] indexFiles = [indexBase + ".bwt",indexBase + ".pac",indexBase + ".sa",indexBase + ".amb",indexBase + ".ann"]
+ }
+ parameter_meta {
+ fasta: "Fasta file to be indexed"
+ constructionAlgorithm: "-a STR BWT construction algorithm: bwtsw, is or rb2 [auto]"
+ blockSize: "-b INT block size for the bwtsw algorithm (effective with -a bwtsw) [10000000]"
+ outputDir: "index will be created in this output directory"
+ }
+}
+
diff --git a/centrifuge.wdl b/centrifuge.wdl
index 9c75f77257b7643c349b243c817499a2477a22cc..3182261156d76793f95e023581178a27026c96db 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -24,10 +24,7 @@ task download {
command {
set -e -o pipefail
${preCommand}
- ${'if [ ! -f ' + seqTaxMapPath +
- ' ]; then mkdir -p ' + seqTaxMapPath +
- '; rm -d ' + seqTaxMapPath +
- '; fi' }
+ ${"mkdir -p $(dirname " + seqTaxMapPath + ")"}
${executable} \
-o ${libraryPath} \
${true='-d ' false='' defined(domain)}${sep=',' domain} \
@@ -92,8 +89,7 @@ task build {
command {
set -e -o pipefail
${preCommand}
- mkdir -p ${centrifugeIndexBase}
- rm -d ${centrifugeIndexBase}
+ ${"mkdir -p $(dirname " + centrifugeIndexBase + ")"}
${centrifugeBuildExecutable} \
${true='--large-index' false='' largeIndex} \
${true='--noauto' false='' noAuto} \
diff --git a/common.wdl b/common.wdl
index 79be3870be1f1d4d932564b42a8263bce1be4ba9..2ac9cb99366ab27e768c29a947bf239064193186 100644
--- a/common.wdl
+++ b/common.wdl
@@ -51,12 +51,13 @@ task concatenateTextFiles {
Array[File] fileList
String combinedFilePath
Boolean? unzip=false
+ Boolean? zip=false
command {
- mkdir -p ${combinedFilePath}
- rm -d ${combinedFilePath}
+ set -e -o pipefail
+ ${"mkdir -p $(dirname " + combinedFilePath + ")"}
${true='zcat' false= 'cat' unzip} ${sep=' ' fileList} \
- > ${combinedFilePath}
+ ${true="| gzip -c" false="" zip} > ${combinedFilePath}
}
output {
diff --git a/cutadapt.wdl b/cutadapt.wdl
index f38f2c3d1ed23097b3c9522de656357fcba27dfe..6e6cd56aa2b028c9c18f08b20c60d162d1cf71f6 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -6,13 +6,13 @@ task cutadapt {
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
+ 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
@@ -59,7 +59,9 @@ task cutadapt {
command {
set -e -o pipefail
- mkdir -p $(dirname ${read1output})
+ ${"mkdir -p $(dirname " + read1output + ")"}
+ ${"mkdir -p $(dirname " + read2output + ")"}
+ ${"mkdir -p $(dirname " + reportPath + ")"}
${preCommand}
cutadapt \
${"--cores=" + cores} \
@@ -120,4 +122,4 @@ task cutadapt {
cpu: select_first([cores])
memory: select_first([memory])
}
-}
\ No newline at end of file
+}
diff --git a/fastqc.wdl b/fastqc.wdl
index 72b4a538358a5fac7c27f6d004ff7a9a026fe4e8..f0fd2fec0371432f054aecd9624dc9bda628f292 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -15,7 +15,11 @@ task fastqc {
File? limits
Int? kmers
String? dir
-
+ # Chops of the .gz extension if present.
+ String name = sub(seqFile, "\\.gz$","")
+ # 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")
command {
set -e -o pipefail
${preCommand}
@@ -40,10 +44,10 @@ task fastqc {
}
output {
- File rawReport = select_first(glob(outdirPath + "/*/fastqc_data.txt"))
- File htmlReport = select_first(glob(outdirPath + "/*/fastqc_report.html"))
- File summary = select_first(glob(outdirPath + "/*/summary.txt"))
- Array[File] images = glob(outdirPath + "/*/Images/*.png")
+ File rawReport = reportDir + "/fastqc_data.txt"
+ File htmlReport = reportDir + "/fastqc_report.html"
+ File summary = reportDir + "/summary.txt"
+ Array[File] images = glob(reportDir + "/Images/*.png")
}
runtime {
@@ -113,4 +117,4 @@ task getConfiguration {
runtime {
memory: 1
}
-}
\ No newline at end of file
+}
diff --git a/samtools.wdl b/samtools.wdl
index 249143ffa7d4215650b6b8dce6d0b2b216548d2b..a1192ac3a08419a8584c01a005cd785649a7d60d 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -65,3 +65,55 @@ task Flagstat {
File flagstat = outputPath
}
}
+
+task fastq {
+ String? preCommand
+ File inputBam
+ String outputRead1
+ String? outputRead2
+ String? outputRead0
+ Int? includeFilter
+ Int? excludeFilter
+ Int? excludeSpecificFilter
+ Boolean? appendReadNumber
+ Boolean? outputQuality
+ Int? compressionLevel
+ Int? threads
+ Int? memory
+ Int totalThreads = select_first([threads, 1])
+
+ command {
+ ${preCommand}
+ samtools fastq \
+ ${true="-1" false="-s" defined(outputRead2)} ${outputRead1} \
+ ${"-2 " + outputRead2} \
+ ${"-0 " + outputRead0} \
+ ${"-f " + includeFilter} \
+ ${"-F " + excludeFilter} \
+ ${"-G " + excludeSpecificFilter} \
+ ${true="-N" false="-n" appendReadNumber} \
+ ${true="-O" false="" outputQuality} \
+ ${"-c " + compressionLevel} \
+ ${"--threads " + totalThreads} \
+ ${inputBam}
+ }
+ output {
+ File read1 = outputRead1
+ File? read2 = outputRead2
+ File? read0 = outputRead0
+ }
+ runtime {
+ cpu: totalThreads
+ memory: select_first([memory, 1])
+ }
+ parameter_meta {
+ preCommand: "A command that is run before the task. Can be used to activate environments"
+ inputBam: "The bam file to process."
+ outputRead1: "If only outputRead1 is given '-s' flag is assumed. Else '-1'."
+ includeFilter: "Include reads with ALL of these flags. Corresponds to '-f'"
+ excludeFilter: "Exclude reads with ONE OR MORE of these flags. Corresponds to '-F'"
+ excludeSpecificFilter: "Exclude reads with ALL of these flags. Corresponds to '-G'"
+ appendReadNumber: "Append /1 and /2 to the read name, or don't. Corresponds to '-n/N"
+
+ }
+}
diff --git a/seqtk.wdl b/seqtk.wdl
new file mode 100644
index 0000000000000000000000000000000000000000..35fbedf368a7d62f1c9ed9643ea96fe0dd7a5a12
--- /dev/null
+++ b/seqtk.wdl
@@ -0,0 +1,26 @@
+task sample {
+ File sequenceFile
+ String? outFilePath = "subsampledReads.fq.gz"
+ String? preCommand
+ Int? seed
+ Boolean? twoPassMode
+ Float? fraction
+ Int? number
+ Boolean? zip = true
+
+ command {
+ set -e -o pipefail
+ ${'mkdir -p $(dirname ' + outFilePath + ')'}
+ ${preCommand}
+ seqtk sample \
+ ${"-s " + seed} \
+ ${true="-2 " false="" twoPassMode} \
+ ${sequenceFile} \
+ ${number} ${fraction} \
+ ${true="| gzip" false="" zip} \
+ ${"> " + outFilePath}
+ }
+ output {
+ File subsampledReads= select_first([outFilePath])
+ }
+}
\ No newline at end of file
diff --git a/spades.wdl b/spades.wdl
new file mode 100644
index 0000000000000000000000000000000000000000..ce9de29cecb0b48d20faff177fc1a007e0e7c312
--- /dev/null
+++ b/spades.wdl
@@ -0,0 +1,80 @@
+task spades {
+ String outputDir
+ String? preCommand
+ File read1
+ File? read2
+ File? interlacedReads
+ File? sangerReads
+ File? pacbioReads
+ File? nanoporeReads
+ File? tslrContigs
+ File? trustedContigs
+ File? untrustedContigs
+ Boolean? singleCell
+ Boolean? metagenomic
+ Boolean? rna
+ Boolean? plasmid
+ Boolean? ionTorrent
+ Boolean? onlyErrorCorrection
+ Boolean? onlyAssembler
+ Boolean? careful
+ Boolean? disableGzipOutput
+ Boolean? disableRepeatResolution
+ File? dataset
+ Int? threads
+ Int? memoryGb
+ File? tmpDir
+ String? k
+ Float? covCutoff
+ Int? phredOffset
+ Int finalThreads = select_first([threads,1])
+ Int totalMemory = select_first([memoryGb, finalThreads * 16])
+ Int clusterMemory = totalMemory / finalThreads
+
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ spades.py \
+ ${"-o " + outputDir} \
+ ${true="--sc" false="" singleCell} \
+ ${true="--meta" false="" metagenomic} \
+ ${true="--rna" false="" rna} \
+ ${true="--plasmid" false="" plasmid} \
+ ${true="--iontorrent" false="" ionTorrent} \
+ ${"--12 " + interlacedReads } \
+ ${true="-1" false="-s" defined(read2)} ${read1} \
+ ${"-2 " + read2 } \
+ ${"--sanger " + sangerReads } \
+ ${"--pacbio " + pacbioReads } \
+ ${"--nanopore " + nanoporeReads } \
+ ${"--tslr " + tslrContigs } \
+ ${"--trusted-contigs " + trustedContigs } \
+ ${"--untrusted-contigs " + untrustedContigs } \
+ ${true="--only-error-correction" false="" onlyErrorCorrection } \
+ ${true="--only-assembler" false="" onlyAssembler } \
+ ${true="--careful" false="" careful } \
+ ${true="--disable-gzip-output" false="" disableGzipOutput} \
+ ${true="--disable-rr" false="" disableRepeatResolution } \
+ ${"--dataset " + dataset } \
+ ${"--threads " + finalThreads} \
+ ${"--memory " + totalMemory } \
+ ${"-k " + k } \
+ ${"--cov-cutoff " + covCutoff } \
+ ${"--phred-offset " + phredOffset }
+ }
+ output {
+ Array[File] correctedReads = glob(outputDir + "/corrected/*.fastq*")
+ File scaffolds = outputDir + "/scaffolds.fasta"
+ File contigs = outputDir + "/contigs.fasta"
+ File assemblyGraphWithScaffoldsGfa = outputDir + "/assembly_graph_with_scaffolds.gfa"
+ File assemblyGraphFastg = outputDir + "/assembly_graph.fastg"
+ File contigsPaths = outputDir + "/contigs.paths"
+ File scaffoldsPaths = outputDir + "/scaffolds.paths"
+ File params = outputDir + "/params.txt"
+ File log = outputDir + "/spades.log"
+ }
+ runtime {
+ cpu: finalThreads
+ memory: clusterMemory
+ }
+}
\ No newline at end of file
diff --git a/unicycler.wdl b/unicycler.wdl
new file mode 100644
index 0000000000000000000000000000000000000000..f7aa36a48067bcd2f880a843d1a4aa401c7f5078
--- /dev/null
+++ b/unicycler.wdl
@@ -0,0 +1,102 @@
+task unicycler {
+ String? preCommand
+ File? short1
+ File? short2
+ File? unpaired
+ File? long
+ String out
+ Int? verbosity
+ Int? minFastaLength
+ Int? keep
+ Boolean? vcf
+ Int? threads
+ Int? memory
+ Int finalThreads = select_first(threads, 1)
+ Int finalMemory = select_first(memory, 4)
+ String? mode
+ Float? minBridgeQual
+ Int? linearSeqs
+ File? spadesPath
+ Boolean? noCorrect
+ Float? minKmerFrac
+ Float? maxKmerFrac
+ Int? kmerCount
+ Float? depthFilter
+ Boolean? noMiniasm
+ File? raconPath
+ File? existingLongReadAssembly
+ Boolean? noRotate
+ File? startGenes
+ Float? startGeneId
+ Float? startGeneCov
+ String? makeblastdbPath
+ File? tblastnPath
+ Boolean? noPilon
+ File? bowtie2Path
+ File? bowtie2buildPath
+ File? samtoolsPath
+ File? pilonPath
+ File? javaPath
+ Int? minPolishSize
+ File? bcftoolsPath
+ Int? minComponentSize
+ Int? minDeadEndSize
+ File? contamination
+ String? scores
+ String? lowScore
+ command {
+ set -e -o pipefail
+ mkdir -p ${out}
+ ${preCommand}
+ unicycler \
+ ${"--short1 " + short1} \
+ ${"--short2 " + short2} \
+ ${"--unpaired " + unpaired} \
+ ${"--long " + long} \
+ --out ${out} \
+ ${"--min_fasta_length " + minFastaLength} \
+ ${"--keep " + keep } \
+ ${true="--vcf" false="" vcf } \
+ ${"--threads " + finalThreads } \
+ ${"--mode " + mode } \
+ ${"--min_bridge_qual " + minBridgeQual } \
+ ${"--linear_seqs " + linearSeqs } \
+ ${"--spades_path " + spadesPath } \
+ ${true="--no_correct" false="" noCorrect } \
+ ${"--min_kmer_frac " + minKmerFrac } \
+ ${"--max_kmer_frac " + maxKmerFrac } \
+ ${"--kmer_count " + kmerCount } \
+ ${"--depth_filter " + depthFilter } \
+ ${true="--no_miniasm" false="" noMiniasm } \
+ ${"--racon_path " + raconPath } \
+ ${"--existing_long_read_assembly " + existingLongReadAssembly } \
+ ${true="--no_rotate" false="" noRotate } \
+ ${"--start_genes " + startGenes } \
+ ${"--start_gene_id " + startGeneId } \
+ ${"--start_gene_cov " + startGeneCov } \
+ ${"--makeblastdb_path " + makeblastdbPath } \
+ ${"--tblastn_path " + tblastnPath } \
+ ${true="--no_pilon" false="" noPilon } \
+ ${"--bowtie2_path " + bowtie2Path } \
+ ${"--bowtie2_build_path " + bowtie2buildPath } \
+ ${"--samtools_path " + samtoolsPath } \
+ ${"--pilon_path " + pilonPath } \
+ ${"--java_path " + javaPath } \
+ ${"--min_polish_size " + minPolishSize } \
+ ${"--bcftools_path " + bcftoolsPath } \
+ ${"--min_component_size " + minComponentSize } \
+ ${"--min_dead_end_size " + minDeadEndSize } \
+ ${"--contamination " + contamination } \
+ ${"--scores " + scores } \
+ ${"--low_score " + lowScore }
+ }
+ output {
+ File assemblyFasta = out + "/assembly.fasta"
+ File assemblyGfa = out + "/assembly.gfa"
+ File log = out + "/unicycler.log"
+ }
+ runtime {
+ cpu: finalThreads
+ memory: finalMemory
+ }
+}
\ No newline at end of file