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imaps-nf's Issues

STAR multimapped bam

make STAR into a subworkflow - allow multimapping then run samtools so that both a single mapped and multimapped bam are outputted.

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.

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.

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