{"id":6307,"projects":[69],"description":"PCAWG EMBL variant calling workflow is developed by European Molecular Biology Laboratory at Heidelberg\n(EMBL, https://www.embl.de), it consists of software components calling structural\nvariants using uniformly aligned tumor / normal WGS sequences. The workflow has been dockerized and packaged\nusing CWL workflow language, the source code is available on GitHub at:\nhttps://github.com/ICGC-TCGA-PanCancer/pcawg_delly_workflow.\n\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 settings.\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==1.0.20170217172322\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, both\nfrom the same donor. Here we assume file names are *tumor_sample.bam* and *normal_sample.bam*, and are\nunder *bams* subfolder.\n\n#### Reference data file\n\nThe workflow also uses one precompiled reference files as input, they can be downloaded from the ICGC Data\nPortal at https://dcc.icgc.org/releases/PCAWG/reference_data/pcawg-dkfz. We assume the reference file is\nunder *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-delly-sv-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\": \"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz\",\n    \"class\": \"File\"\n  },\n  \"reference-gc\": {\n    \"path\": \"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-delly/hs37d5_1000GP.gc\",\n    \"class\": \"File\"\n  },\n  \"somatic_sv_vcf\": {\n    \"path\":\"delly.somatic.sv.vcf.gz\",\n    \"class\":\"File\"\n  },\n  \"somatic_bedpe\": {\n    \"path\":\"delly.somatic.sv.bedpe.txt\",\n    \"class\":\"File\"\n  },\n  \"cov\": {\n    \"path\":\"delly.sv.cov.tar.gz\",\n    \"class\":\"File\"\n  },\n  \"cov_plots\": {\n    \"path\":\"delly.sv.cov.plots.tar.gz\",\n    \"class\":\"File\"\n  },\n  \"germline_sv_vcf\": {\n    \"path\":\"delly.germline.sv.vcf.gz\",\n    \"class\":\"File\"\n  },\n  \"germline_bedpe\": {\n    \"path\":\"delly.germline.sv.bedpe.txt\",\n    \"class\":\"File\"\n  },\n  \"sv_log\": {\n    \"path\":\"delly.sv.log.tar.gz\",\n    \"class\":\"File\"\n  },\n  \"sv_timing\": {\n    \"path\":\"delly.sv.timing.json\",\n    \"class\":\"File\"\n  },\n  \"sv_qc\": {\n    \"path\":\"delly.sv.qc.json\",\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-delly-sv-caller.cwl \"https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/pcawg_delly_workflow/2.0.1-cwl1.0/delly_docker/Dockstore.cwl\"\n```\n\n- Run `cwltool` to execute the workflow\n```\nnohup cwltool --debug --non-strict pcawg-delly-sv-caller.cwl pcawg-delly-sv-caller.job.json > pcawg-delly-sv-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_delly_workflow","url":"https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fpancancer%2Fpcawg_delly_workflow","authors":[1],"rubrics":[25]}