github.com/pachyderm/pachyderm@v1.13.4/examples/gatk/joint-call.json (about)

     1  {
     2    "pipeline": {
     3      "name": "joint_call"
     4    },
     5    "description": "A pipeline that performs joint genotyping of multiple samples.",
     6    "transform": {
     7      "image": "broadinstitute/gatk3:3.8-0",
     8      "cmd": [ "/bin/bash" ],
     9      "stdin": [
    10          "files=\"\"",
    11          "for f in /pfs/likelihoods/*",
    12          "do",
    13          "filename=$(basename \"$f\")",
    14          "extension=\"${filename##*.}\"",
    15          "echo $extension",
    16          "if [ \"$extension\" == \"vcf\" ]",
    17          "then",
    18          "files=\"$files -V $f\"",
    19          "fi",
    20          "done",
    21  	"java -jar /usr/GenomeAnalysisTK.jar -T GenotypeGVCFs -R /pfs/reference/ref.fasta $files -o /pfs/out/joint.vcf -L 20:10,000,000-10,200,000"
    22      ]
    23    },
    24    "parallelism_spec": {
    25      "constant": "1"
    26    },
    27    "input": {
    28      "cross": [
    29        {
    30          "pfs": {
    31            "repo": "reference",
    32            "glob": "/"
    33          }
    34        },
    35        {
    36          "pfs": {
    37            "repo": "likelihoods",
    38            "glob": "/"
    39          }
    40        }
    41      ]
    42    }
    43  }