{"id":6299,"projects":[69],"description":"PCAWG DKFZ variant calling workflow is developed by German Cancer Research Center\n(DKFZ, https://www.dkfz.de), it consists of software components calling somatic substitutions, indels\nand copy number variations using uniformly aligned tumor / normal WGS sequences. The workflow has been\ndockerized and packaged using CWL workflow language, the source code is available on\nGitHub at: https://github.com/ICGC-TCGA-PanCancer/dkfz_dockered_workflows.\n\nThis workflow has been tested using cwltool version *1.0.20180116213856*. Newer cwltool may not work.\n\n## Run the workflow with your own data\n\n### Prepare compute environment and install software packages\nThe workflow has been tested in Ubuntu 16.04 Linux environment with the following hardware and software\nsettings.\n\n#### Hardware requirement (assuming 30X coverage whole genome sequence)\n- CPU core: 16\n- Memory: 64GB\n- Disk space: 1TB\n\n#### Software installation\n- Docker (1.12.6): follow instructions to install Docker https://docs.docker.com/engine/installation\n- CWL tool\n```\npip install cwltool==1.0.20180116213856\n```\n\n### Prepare input data\n#### Input aligned tumor / normal BAM files\n\nThe workflow uses a pair of aligned BAM files as input, one BAM for tumor, the other for normal,\nboth from the same donor. Here we assume file names are *tumor_sample.bam* and *normal_sample.bam*,\nand are under *bams* subfolder.\n\n#### Dependent structural variant file\nThis is a file produced by EMBL (aka DELLY) structural variation calling workflow. Please follow instruction\n[here](https://dockstore.org/containers/quay.io/pancancer/pcawg_delly_workflow) to run EMBL workflow\nto get the *run_id.embl-delly.somatic.sv.bedpe.txt* file.\n\n#### Reference data file\n\nThe workflow also uses one precompiled reference file (*dkfz-workflow-dependencies_150318_0951.tar.gz*) as input,\nthey can be downloaded from the ICGC Data Portal under https://dcc.icgc.org/releases/PCAWG/reference_data/pcawg-dkfz.\nWe assume the reference file is under *reference* subfolder.\n\n#### Job JSON file for CWL\n\nFinally, we need to prepare a JSON file with input, reference and output files specified. Please replace\nthe *tumor* and *normal* parameters with your real BAM file names. Parameters for output are file name\nsuffixes, usually don't need to be changed.\n\nName the JSON file: *pcawg-dkfz-variant-caller.job.json*\n```\n{\n  \"run-id\": \"run_id\",\n  \"tumor-bam\": {\n    \"path\":\"bams/tumor_sample.bam\",\n    \"class\":\"File\"\n  },\n  \"normal-bam\": {\n    \"path\":\"bams/normal_sample.bam\",\n    \"class\":\"File\"\n  },\n  \"reference-gz\": {\n    \"path\": \"reference/dkfz-workflow-dependencies_150318_0951.tar.gz\",\n    \"class\": \"File\"\n  },\n  \"delly-bedpe\":\n  {\n    \"path\":\"delly-bedpe/run_id.embl-delly.somatic.sv.bedpe.txt\",\n    \"class\":\"File\"\n  },\n  \"germline_indel_vcf_gz\": {\n    \"path\": \"germline.indel.vcf.gz\",\n    \"class\": \"File\"\n  },\n  \"somatic_snv_mnv_vcf_gz\": {\n    \"path\": \"somatic.snv.mnv.vcf.gz\",\n    \"class\": \"File\"\n  },\n  \"germline_snv_mnv_vcf_gz\": {\n    \"path\": \"germline.snv.mnv.vcf.gz\",\n    \"class\": \"File\"\n  },\n  \"somatic_cnv_tar_gz\": {\n    \"path\": \"somatic.cnv.tar.gz\",\n    \"class\": \"File\"\n  },\n  \"somatic_cnv_vcf_gz\": {\n    \"path\": \"somatic.cnv.vcf.gz\",\n    \"class\": \"File\"\n  },\n  \"somatic_indel_tar_gz\": {\n    \"path\": \"somatic.indel.tar.gz\",\n    \"class\": \"File\"\n  },\n  \"somatic_snv_mnv_tar_gz\": {\n    \"path\": \"somatic.snv.mnv.tar.gz\",\n    \"class\": \"File\"\n  },\n  \"somatic_indel_vcf_gz\": {\n    \"path\": \"somatic.indel.vcf.gz\",\n    \"class\": \"File\"\n  }\n}\n```\n\n### Run the workflow\n#### Option 1: Run with CWL tool\n- Download CWL workflow definition file\n```\nwget -O pcawg-dkfz-variant-caller.cwl \"https://github.com/ICGC-TCGA-PanCancer/dkfz_dockered_workflows/blob/2.0.2_cwl1.0/Dockstore.cwl\"\n```\n\n- Run `cwltool` to execute the workflow\n```\nnohup cwltool --debug --non-strict pcawg-dkfz-variant-caller.cwl pcawg-dkfz-variant-caller.job.json > pcawg-dkfz-variant-caller.log 2>&1 &\n```\n\n#### Option 2: Run with the Dockstore CLI\nSee the *Launch with* section below for details.","image":"","tags":"","type":"","title":"pcawg-dkfz-workflow","url":"https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fpancancer%2Fpcawg-dkfz-workflow","authors":[1],"rubrics":[25]}