README.md

gdc-workflow-cwl-v1

Docker

Docker need to be installed before running the tools.

Rabix

These cwl tools are created by Rabix Composer (1.0.0-rc.1) and by using the rabix-1.0.0-rc2 can run locally.

usage: rabix *.cwl input.json

Example for workflow-input : fastq2cram-workflow-input.json

{
    "reference" : {
      "location" : "/Users/zhangb1/Documents/Tools/CWL.V1/exampleFASTA.fasta",
      "class" : "File"
    },
   "read_group": "'@RG\\tID:test\\tSM:cwl-test'",
   "output_bam": "test.sort.rd.bam",
   "output_cram": "test.sort.rd.cram",
    "input1" :  {
      "location" : "/Users/zhangb1/Documents/cavatica/GRCh37/test3_normal_1.fq.gz",
      "class" : "File"
    }, 
    "input2" : {
      "location" : "/Users/zhangb1/Documents/cavatica/GRCh37/test3_normal_2.fq.gz",
      "class" : "File"
      }
  
}

CAVATICA

These cwl.v1 also can be imported to CAVATICA by using Rabix Composer.

(Testing...)