Introduction
CWL Workflow for producing genomic alignment files (BAM) from compressed FASTQ files having unique molecular index
This is the workflow is written using Common Workflow Language (CWL) version 1.0 (https://www.commonwl.org/v1.0/) and is used at Memorial Sloan Kettering Cancer Center for producing standard bam files from the NY state-approved MSK-ACCESS assay.
It is meant to be run on a single sample paired-end FASTQ with unique molecular index(UMI), from Illumina sequencing data, but maybe generalizable to other sequencing platforms and sequencing panels as well, which produce paired-end data with UMIs.
For documentation visit: https://msk-access.gitbook.io/uncollapsed-bam-generation/
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