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- task samtools {
- File bam_file
- String bam_id=basename(bam_file)
- String docker
- String cluster
- String disk_size
-
-
- command <<<
- samtools index --help
- samtools index -b ${bam_file} > ./${bam_id}.bai
- cp ${bam_file} ./
- >>>
-
- runtime {
- docker: docker
- cluster: cluster
- systemDisk: "cloud_ssd 40"
- dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
- }
-
- output {
- File bam="${bam_id}"
- File bam_index="${bam_id}.bai"
- }
-
- }
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