arriba2/tasks/arriba.wdl

task arriba {
  String sample_id
  File fastq1
  File fastq2
  File STAR_INDEX_DIR
  File ASSEMBLY_FA
  File ANNOTATION_GTF

  String docker
  String cluster
  String disk_size


  command <<<
	
    set -o pipefail
    set -e

    mkdir ./output/
    STAR \
      --runThreadN 4 \
      --genomeDir ${STAR_INDEX_DIR} \
      --genomeLoad NoSharedMemory \
      --readFilesIn ${fastq1} ${fastq2} \
      --readFilesCommand zcat \
      --outStd BAM_Unsorted \
      --outSAMtype BAM Unsorted \
      --outSAMunmapped Within \
      --outBAMcompression 0 \
      --outFilterMultimapNmax 50 \
      --peOverlapNbasesMin 10 \
      --alignSplicedMateMapLminOverLmate 0.5 \
      --alignSJstitchMismatchNmax 5 -1 5 5 \
      --chimSegmentMin 10 \
      --chimOutType WithinBAM HardClip \
      --chimJunctionOverhangMin 10 \
      --chimScoreDropMax 30 \
      --chimScoreJunctionNonGTAG 0 \
      --chimScoreSeparation 1 \
      --chimSegmentReadGapMax 3 \
      --chimMultimapNmax 50 |tee ./output/${sample_id}.Aligned.out.bam |/arriba_v2.1.0/arriba \
      -x /dev/stdin \
      -o ./output/${sample_id}_fusions.tsv \
      -O ./output/${sample_id}_fusions.discarded.tsv \
      -a ${ASSEMBLY_FA} \
      -g ${ANNOTATION_GTF} \
      -b /arriba_v2.1.0/database/blacklist_hg38_GRCh38_v2.1.0.tsv.gz \
      -k /arriba_v2.1.0/database/known_fusions_hg38_GRCh38_v2.1.0.tsv.gz \
      -t /arriba_v2.1.0/database/known_fusions_hg38_GRCh38_v2.1.0.tsv.gz \
      -p /arriba_v2.1.0/database/protein_domains_hg38_GRCh38_v2.1.0.gff3

    
  >>>
	
  runtime {
    docker: docker
    cluster: cluster
    systemDisk: "cloud_ssd 40"
    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  }

  output {
    Array[File] arriba_result = glob("./output/*.tsv")
    Array[File] arriba_bam=glob("./output/*.bam")
  }
}