github.com/pachyderm/pachyderm@v1.13.4/examples/gatk/likelihoods.json (about)

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