[FEATURE] split freebayes input relying on BAM size - Githubissues

cnr-ibba / nf-modules

Custom Nextflow DSL2 modules

MIT License

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[FEATURE] split freebayes input relying on BAM size #17

Closed bunop closed 2 years ago

bunop commented 2 years ago

Is your feature request related to a problem? Please describe

Is difficult to tune freebayes/parallel step when having a lot of samples.

Describe the solution you'd like

Try to utilize a different approach using split_ref_by_bai_datasize.py

Describe alternatives you've considered

Another method could be use coverage_to_regions.py, however this seems to work on single .bam files

Additional context

[x] Implement a freebayes custom image (biocontainers lacks of numpy and scipy dependencies)
[x] Use split_ref_by_bai_datasize.py in freebayes multi step
[x] Move freebayes/parallel into freebayes/single
[x] Use coverage_to_regions.py in freebayes single step