imaps-nf's People
imaps-nf's Issues
Choice of peak caller
Clippy should be default peak caller, but users should be able to choose between paralcu, clippy and icount at run time - similar to how they can choose the specific genome version they want to use. choice of peak caller impacts downstream outputs that depend on peak calling, namely peka.
STAR multimapped bam
make STAR into a subworkflow - allow multimapping then run samtools so that both a single mapped and multimapped bam are outputted.
Update clippy container
Once new updates are made to Clippy update the Clippy container in clippy module to latest version with latest tested defaults.
Parameters for programs
parameters need to be set correctly and editable parameters need to be exposed to the user.
Add PEKA to pipeline
Latest version of PEKA needs to be added to pipeline
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