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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's with unique molecular index(UMI), from Illumina sequencing data, but may be 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/
