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 Unicycler {
    input {
        String out

        String? preCommand
        File? short1
        File? short2
        File? unpaired
        File? long
        Int? verbosity
        Int? minFastaLength
        Int? keep
        Boolean? vcf
        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

        Int threads = 1
        String memory = "4GiB"
    }

    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 " + threads } \
        ~{"--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: threads
        memory: memory
    }
}