pcawg-dkfz-workflow

PCAWG DKFZ variant calling workflow is developed by German Cancer Research Center (DKFZ, https://www.dkfz.de), it consists of software components calling somatic substitutions, indels and copy number variations 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/dkfz_dockered_workflows. This workflow has been tested using cwltool version *1.0.20180116213856*. Newer cwltool may not work. ## 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==1.0.20180116213856 ``` ### 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. #### Dependent structural variant file This is a file produced by EMBL (aka DELLY) structural variation calling workflow. Please follow instruction [here](https://dockstore.org/containers/quay.io/pancancer/pcawg_delly_workflow) to run EMBL workflow to get the *run_id.embl-delly.somatic.sv.bedpe.txt* file. #### Reference data file The workflow also uses one precompiled reference file (*dkfz-workflow-dependencies_150318_0951.tar.gz*) as input, they can be downloaded from the ICGC Data Portal under 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-dkfz-variant-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": "reference/dkfz-workflow-dependencies_150318_0951.tar.gz", "class": "File" }, "delly-bedpe": { "path":"delly-bedpe/run_id.embl-delly.somatic.sv.bedpe.txt", "class":"File" }, "germline_indel_vcf_gz": { "path": "germline.indel.vcf.gz", "class": "File" }, "somatic_snv_mnv_vcf_gz": { "path": "somatic.snv.mnv.vcf.gz", "class": "File" }, "germline_snv_mnv_vcf_gz": { "path": "germline.snv.mnv.vcf.gz", "class": "File" }, "somatic_cnv_tar_gz": { "path": "somatic.cnv.tar.gz", "class": "File" }, "somatic_cnv_vcf_gz": { "path": "somatic.cnv.vcf.gz", "class": "File" }, "somatic_indel_tar_gz": { "path": "somatic.indel.tar.gz", "class": "File" }, "somatic_snv_mnv_tar_gz": { "path": "somatic.snv.mnv.tar.gz", "class": "File" }, "somatic_indel_vcf_gz": { "path": "somatic.indel.vcf.gz", "class": "File" } } ``` ### Run the workflow #### Option 1: Run with CWL tool - Download CWL workflow definition file ``` wget -O pcawg-dkfz-variant-caller.cwl "https://github.com/ICGC-TCGA-PanCancer/dkfz_dockered_workflows/blob/2.0.2_cwl1.0/Dockstore.cwl" ``` - Run `cwltool` to execute the workflow ``` nohup cwltool --debug --non-strict pcawg-dkfz-variant-caller.cwl pcawg-dkfz-variant-caller.job.json > pcawg-dkfz-variant-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-dk...