Pipeline definition { "name": "samtools index", "description": "Run samtools index to generate a BAM index file", "inputParameters": [ {"name": "inputFile", "localCopy": { "disk": "data", "path": "input.bam" } }, {"name": "outputFile", "localCopy": { "disk": "data", "path": "output.bam.bai" } }, ], "resources": { "minimumCpuCores": 1, "minimumRamGb": 1, "disks": [{ "name": "data", "type": "PERSISTENT_HDD" "sizeGb": 200, "mountPoint": "/mnt/data", }] }, "docker": { "imageName": "quay.io/cancercollaboratory/dockstore-tool-samtools-index", "cmd": "samtools index /mnt/data/input.bam /mnt/data/output.bam.bai" } }