spades.wdl

version 1.0

# Copyright (c) 2017 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
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.

task Spades {
    input {
        File read1
        File? read2
        String outputDir

        String? preCommand
        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
        File? tmpDir
        String? k
        Float? covCutoff
        Int? phredOffset

        Int threads = 1
        Int memoryGb = 16
    }

    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 " + 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 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: threads
        memory: "~{memoryGb}G"
    }
}