pcawg-bwa-mem-workflow

PCAWG uniform alignment workflow uses the popular short read aligner tool BWA MEM (https://github.com/lh3/bwa) with BioBAMBAM (https://github.com/gt1/biobambam) for BAM sorting, merging and marking duplicate. The alignment workflow has been dockerized and packaged using CWL workflow language, the source code is available on GitHub at: https://github.com/ICGC-TCGA-PanCancer/Seqware-BWA-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 unaligned BAM files The workflow uses lane-level unaligned BAM files as input, one BAM per lane (aka read group). Please ensure *@RG* field is populated properly in the BAM header, the following is a valid *@RG* entry. *ID* field has to be unique among your dataset. ``` @RG ID:WTSI:9399_7 CN:WTSI PL:ILLUMINA PM:Illumina HiSeq 2000 LB:WGS:WTSI:28085 PI:453 SM:f393ba16-9361-5df4-e040-11ac0d4844e8 PU:WTSI:9399_7 DT:2013-03-18T00:00:00+00:00 ``` Multiple unaligned BAMs from the same sample (with same *SM* value) should be run together. *SM* is globally unique UUID for the sample. Put the input BAM files in a subfolder. In this example, we have two BAMs in a folder named *bams*. #### Reference genome sequence files The reference genome files can be downloaded from the ICGC Data Portal at under https://dcc.icgc.org/releases/PCAWG/reference_data/pcawg-bwa-mem. Please download all reference files and put them under a subfolder called *reference*. #### Job JSON file for CWL Finally, we need to prepare a JSON file with input, reference and output files specified. Please replace the *reads* parameter with your real BAM file name. Name the JSON file: *pcawg-bwa-mem-aligner.job.json* ``` { "reads": [ { "path":"bams/seq_from_normal_sample_A.lane_1.bam", "class":"File" }, { "path":"bams/seq_from_normal_sample_A.lane_2.bam", "class":"File" } ], "output_dir": "datastore", "output_file_basename": "seq_from_normal_sample_A", "reference_gz_amb": { "path": "reference/genome.fa.gz.64.amb", "class": "File" }, "reference_gz_sa": { "path": "reference/genome.fa.gz.64.sa", "class": "File" }, "reference_gz_pac": { "path": "reference/genome.fa.gz.64.pac", "class": "File" }, "reference_gz_ann": { "path": "reference/genome.fa.gz.64.ann", "class": "File" }, "reference_gz_bwt": { "path": "reference/genome.fa.gz.64.bwt", "class": "File" }, "reference_gz_fai": { "path": "reference/genome.fa.gz.fai", "class": "File" }, "reference_gz": { "path": "reference/genome.fa.gz", "class": "File" } } ``` ### Run the workflow #### Option 1: Run with CWL tool - Download CWL workflow definition file ``` wget -O pcawg-bwa-mem-aligner.cwl "https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/Seqware-BWA-Workflow/2.6.8_1.3/Dockstore.cwl" ``` - Run *cwltool* to execute the workflow ``` nohup cwltool --debug --non-strict pcawg-bwa-mem-aligner.cwl pcawg-bwa-mem-aligner.job.json > pcawg-bwa-mem-aligner.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-bw...

View Associations