pcawg_delly_workflow

PCAWG EMBL variant calling workflow is developed by European Molecular Biology Laboratory at Heidelberg (EMBL, https://www.embl.de), it consists of software components calling structural variants using uniformly aligned tumor / normal WGS sequences. The workflow has been dockerized and packaged using CWL workflow language, the source code is available on GitHub at: https://github.com/ICGC-TCGA-PanCancer/pcawg_delly_workflow. ## Run the workflow with your own data ### Prepare compute environment and install software packages The workflow has been tested in Ubuntu 16.04 Linux environment with the following hardware and software settings. #### Hardware requirement (assuming 30X coverage whole genome sequence) - CPU core: 16 - Memory: 64GB - Disk space: 1TB #### Software installation - Docker (1.12.6): follow instructions to install Docker https://docs.docker.com/engine/installation - CWL tool ``` pip install cwltool==1.0.20170217172322 ``` ### Prepare input data #### Input aligned tumor / normal BAM files The workflow uses a pair of aligned BAM files as input, one BAM for tumor, the other for normal, both from the same donor. Here we assume file names are *tumor_sample.bam* and *normal_sample.bam*, and are under *bams* subfolder. #### Reference data file The workflow also uses one precompiled reference files as input, they can be downloaded from the ICGC Data Portal at https://dcc.icgc.org/releases/PCAWG/reference_data/pcawg-dkfz. We assume the reference file is under *reference* subfolder. #### Job JSON file for CWL Finally, we need to prepare a JSON file with input, reference and output files specified. Please replace the *tumor* and *normal* parameters with your real BAM file names. Parameters for output are file name suffixes, usually don't need to be changed. Name the JSON file: *pcawg-delly-sv-caller.job.json* ``` { "run-id": "run_id", "tumor-bam": { "path":"bams/tumor_sample.bam", "class":"File" }, "normal-bam": { "path":"bams/normal_sample.bam", "class":"File" }, "reference-gz": { "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz", "class": "File" }, "reference-gc": { "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-delly/hs37d5_1000GP.gc", "class": "File" }, "somatic_sv_vcf": { "path":"delly.somatic.sv.vcf.gz", "class":"File" }, "somatic_bedpe": { "path":"delly.somatic.sv.bedpe.txt", "class":"File" }, "cov": { "path":"delly.sv.cov.tar.gz", "class":"File" }, "cov_plots": { "path":"delly.sv.cov.plots.tar.gz", "class":"File" }, "germline_sv_vcf": { "path":"delly.germline.sv.vcf.gz", "class":"File" }, "germline_bedpe": { "path":"delly.germline.sv.bedpe.txt", "class":"File" }, "sv_log": { "path":"delly.sv.log.tar.gz", "class":"File" }, "sv_timing": { "path":"delly.sv.timing.json", "class":"File" }, "sv_qc": { "path":"delly.sv.qc.json", "class":"File" } } ``` ### Run the workflow #### Option 1: Run with CWL tool - Download CWL workflow definition file ``` wget -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" ``` - Run `cwltool` to execute the workflow ``` nohup cwltool --debug --non-strict pcawg-delly-sv-caller.cwl pcawg-delly-sv-caller.job.json > pcawg-delly-sv-caller.log 2>&1 & ``` #### Option 2: Run with the Dockstore CLI See the *Launch with* section below for details.

URL(s):

• https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fpancancer%2Fpcawg_de...