warp/all_of_us/rna_seq/AggregateSusieWorkflow.wdl at 63a9c15b3f5902eba0ac2d7edab067c90d9e85be · broadinstitute/warp · GitHub

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version 1.0

task AggregateSusie{
    input{
        #Array[File] SusieParquets
        File SusieParquetsFOFN
        Int Memory
        String OutputPrefix
        Int NumThreads
    }

    command <<<
    set -euo pipefail
    export GSUTIL_PARALLEL_PROCESS_COUNT=32
    export GSUTIL_PARALLEL_THREAD_COUNT=8

    awk '{print $1}' ~{SusieParquetsFOFN} | grep -v '^$' > file_paths.txt

    mkdir -p localized
    gsutil -m cp -I localized/ < file_paths.txt

    # Write the new local file paths into filelist.txt
    ls -1 "$(pwd)/localized/*" > filelist.txt
    Rscript /tmp/merge_susie.R --FilePaths file_paths.txt  --OutputPrefix ~{OutputPrefix}
    >>>

    runtime {
    # the docker sha that the workflow ran with is:
    # ghcr.io/aou-multiomics-analysis/aggregate_susie@sha256:ede17b5112eadb765f22cdfbd2a987da96087a1e2f0ad224994c16f1af645443
        docker: "ghcr.io/aou-multiomics-analysis/aggregate_susie:main@sha256:ede17b5112eadb765f22cdfbd2a987da96087a1e2f0ad224994c16f1af645443"
        disks: "local-disk 500 SSD"
        memory: "~{Memory}GB"
        cpu: "~{NumThreads}"
    }


    output {
        File MergedSusieParquet = "${OutputPrefix}_SusieMerged.parquet"
        File MergedSusieTsv = "${OutputPrefix}_SusieMerged.tsv.gz"
    }

}


task AnnotateSusie {
    input {
        File SusieTSV
        File GencodeGTF
        File PlinkAfreq
        String OutputPrefix
        Int Memory
        File AnnotationENCODE
        File AnnotationFANTOM5
        File AnnotationVEP
        File AnnotationVEPIndex
        File AnnotationGnomad
        File AnnotationPhyloP


    }
    command <<<
    set -euo pipefail
    Rscript /tmp/annotate_susie_data.R \
        --OutputPrefix ~{OutputPrefix} \
        --GencodeGTF ~{GencodeGTF} \
        --PlinkAfreq ~{PlinkAfreq} \
        --SusieTSV ~{SusieTSV} \
        --phyloPBigWig ~{AnnotationPhyloP} \
        --FANTOM5 ~{AnnotationFANTOM5} \
        --gnomadConstraint ~{AnnotationGnomad} \
        --ENCODEcCRES ~{AnnotationENCODE} \
        --VEPAnnotationsTable ~{AnnotationVEP}
    >>>
   runtime {
        docker: "ghcr.io/aou-multiomics-analysis/aggregate_susie:main@sha256:ede17b5112eadb765f22cdfbd2a987da96087a1e2f0ad224994c16f1af645443"
        disks: "local-disk 500 SSD"
        memory: "~{Memory}GB"
        cpu: "1"
    }


    output {
        File AnnotatedSusieParquetOut = "~{OutputPrefix}_SusieMerged.annotated.tsv"
    }

}


workflow AggregateSusieWorkflow {
    input {
        #Array[File] SusieParquets
        File SusieParquetsFOFN
        Int Memory
        String OutputPrefix
        Int NumThreads

        File GencodeGTF
        File PlinkAfreq
        File AnnotationPhyloP
        File AnnotationENCODE
        File AnnotationFANTOM5
        File AnnotationVEP
        File AnnotationGnomad
        File AnnotationVEPIndex

    }

    String pipeline_version = "aou_9.0.2"

    call AggregateSusie {
        input:
            SusieParquetsFOFN = SusieParquetsFOFN,
            OutputPrefix = OutputPrefix,
            Memory = Memory,
            NumThreads = NumThreads
    }

    call AnnotateSusie {
        input:
            SusieTSV = AggregateSusie.MergedSusieTsv,
            GencodeGTF = GencodeGTF,
            PlinkAfreq = PlinkAfreq,
            OutputPrefix = OutputPrefix,
            Memory = Memory,
            AnnotationPhyloP = AnnotationPhyloP,
            AnnotationENCODE = AnnotationENCODE,
            AnnotationFANTOM5 = AnnotationFANTOM5,
            AnnotationVEP = AnnotationVEP,
            AnnotationVEPIndex = AnnotationVEPIndex,
            AnnotationGnomad = AnnotationGnomad
    }

    output {
        File AnnotatedMergedSusieParquet = AnnotateSusie.AnnotatedSusieParquetOut
        #File MergedSusieParquet = AggregateSusie.MergedSusieParquet
        #File MergedSusieTsv = AggregateSusie.MergedSusieTsv
    }

}