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- task battenberg {
- String sample_id
- File tumor_bam
- String normal_id
- File normal_bam
-
- String docker
- String cluster
- String disk_size
-
- command <<<
-
- set -o pipefail
- set -e
- cp ${normal_bam} ./${normal_id}.bam
- cp ${tumor_bam} ./${sample_id}.bam
-
- /opt/conda/envs/samtools/bin/samtools view -h -@ 16 -o ${normal_id}.sorted.deduped.sam ./${normal_id}.bam
-
- >>>
-
- runtime {
- docker : docker
- cluster: cluster
- systemDisk: "cloud_ssd 40"
- dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
- }
-
- output {
- File normal_bam_data = "${normal_id}.sorted.deduped.sam"
- }
-
- }
-
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