Asmultipcf implementation for multi-sample ASCAT CNV calling #1646
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Made changes that document usage of WES references from the ASCAT developers and how to avoid a null pointer error
…ascat Update usage.md
Updated CHANGELOG
Update CHANGELOG.md
adding new module asmultipcf to modify ascat to work on multisample contexts
Adding change that includes both a new parameter for asmultipcf and passes it to the existing ascat subworkflow grouped by patient.
Drafting changes to the ASCAT module to layer asmultipcf downstream once ascat is done running.
Making changes to have it use nextflow to run all samples ascat first before proceeding with multi, drawing inspiration from the joint_mutect2 implementation
…lled back to PSC to use my own test set there
Updating change log for ASCAT asmultipcf
Updating relevant usage docs for asmultipcf implementation
…into asmultipcf Made changes to documentation on Github but made changes to nf-core lint and other issues locally, hence the merge.
alexanderchang1
requested review from
FriederikeHanssen and
maxulysse
as code owners
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PR checklist
I implemented the multi-sample ASCAT by adding a check so that if the flag is True, like joint_mutect2, it runs asmultipcf as a local module afterwards to create an additional result. I've added a test based on the structure of the ascat test but don't have access to the actual sequencing files and was unable to test it.
My institutional cluster doesn't allow docker so I ran it with the apptainer test instead when debugging and checking.
Can you help me with the test? Everything else I've tried in pieces locally but I'm not familiar with how to access the specific files that are mentioned in the test files.
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/output.mdis updated.CHANGELOG.mdis updated.