msk-access / uncollapsed_bam_generation

Workflow for making MSK-ACCESS standard binary alignment mapping file.

description
CWL Workflow for producing genomic alignment files (BAM) from compressed FASTQ files having unique molecular index

Un-collapsed Binary Alignment Map (BAM) file Generation

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/

uncollapsed_bam_generation's Issues

Test data

Determine test data from standard bam file creation which can be used for testing workflow and CI

consolidate create_bam_index params

abra_bam_index_flag
create_bam_index
create_bam_index_1

Singularity build files are getting written to /tmp

Maybe they aren't large enough to pose an issue? But still, probably better to not use /tmp at all

jx19.cbio.private

/tmp/.singularity-build.seIIYk
/tmp/.singularity-build.seIIYk/etc
/tmp/.singularity-build.seIIYk/etc/hosts
/tmp/.singularity-build.seIIYk/etc/adduser.conf
/tmp/.singularity-build.seIIYk/etc/alternatives

Initial Update

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Once you have closed it, the bot will open pull requests for updates as soon as they are available.

Upgrade Standard BAM Generation Workflow

Upgrade CWL to the new version using the Flowchart attached and using the Standard Bam Generation Section in the Flowchart.

Note: Flowchart with contents in Teal color are to be taken from cwl-commandlinetools and the rest are from cwl_subworkflows.

• CWL
• Readme
• Example Input
• Update Gitbook

Testing standard bam processing

We need to test the workflow at following.

• Update the cwl on cwl-commandlinetools such that the output id per tools are unique when we run the workflow.
• Test the workflow on JUNO using cwltool and toil-cwl-runner
• Test the workflow on github using toil-cwl-runner for continuous integration using TravisCI or AppVeyor or CircleCI with python pytest or unittest.

Write documentation for standard bam processiong