AscatNgs rule has genome version and threading hard coded - Githubissues

Clinical-Genomics / BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

https://balsamic.readthedocs.io/

MIT License

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AscatNgs rule has genome version and threading hard coded #767

Closed hassanfa closed 3 years ago

hassanfa commented 3 years ago

Pretty much title.

The following lines are affected:

https://github.com/Clinical-Genomics/BALSAMIC/blob/72b633a8badbd557b01ad68252dc49f93789a630/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule#L146

https://github.com/Clinical-Genomics/BALSAMIC/blob/72b633a8badbd557b01ad68252dc49f93789a630/BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule#L147

Solution:

Extract genome version from config
Extract threading the same way as other rules (i.e. params)

ashwini06 commented 3 years ago

Fixed in #784