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task spades {
String outputDir
String? preCommand
File? read1
File? read2
File? singleRead
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 = 1
Int? memoryGb = 4
File? tmpDir
String? k
Float? covCutoff
Int? phredOffset
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 }
${"--threads " + threads } \
${"-1 " + read1 } \
${"-2 " + read2 } \
${"-s " + singleRead } \
${"--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 " + threads } \
${"--memory " + memoryGb } \
${"-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 assemblyGraphGfa = outputDir + "/assembly_graph.gfa"
File assemblyGraphFastg = outputDir + "/assembly_graph.fastq"
File contigsPaths = outputDir + "/contigs.paths"
File scaffoldsPaths = outputDir + "/scaffolds.paths"
File params = outputDir + "/params.txt"
File log = outputDir + "/spades/log"
}
runtime {
cpu: select_first([threads])
memory: select_first([memoryGb]) + "G"
}
}