task suppa2{ String sample_id File fastq1 File fastq2 File suppa2_GTF File suppa2_ioe File salmon_index String docker String cluster String disk_size command <<< set -o pipefail set -e /software/salmon-1.5.2_linux_x86_64/bin/salmon quant -i ${salmon_index} -l A --gcBias -1 ${fastq1} -2 ${fastq2} -p 16 -o ./${sample_id}_salmon multipleFieldSelection.py -i ./${sample_id}_salmon/quant.sf -k 1 -f 4 -o ${sample_id}_iso_tpm.txt sed 's@|ENSG.*|@@' ${sample_id}_iso_tpm.txt > ${sample_id}_iso_tpm_formatted.txt suppa.py psiPerEvent -i ${suppa2_ioe} -e ${sample_id}_iso_tpm_formatted.txt -o ${sample_id}_events suppa.py psiPerIsoform -g ${suppa2_GTF} -e ${sample_id}_iso_tpm_formatted.txt -o ${sample_id} >>> runtime { docker : docker cluster: cluster systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File suppa2_events = "${sample_id}_events.psi" File suppa2_isoform = "${sample_id}_events.psi" File TPM = "${sample_id}_iso_tpm.txt" File formatted_TPM = "${sample_id}_iso_tpm_formatted.txt" } }