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frattalab / PAPA

PAPA (Pipeline-Alternative Polyadenylation) - Snakemake pipeline for analysis of APA from short-read RNA-seq data
GNU General Public License v3.0
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Optionally pass additional command line flags to Salmon quant #43

Closed SamBryce-Smith closed 1 year ago

SamBryce-Smith commented 1 year ago

Currently bias correction flags are hardcoded in the salmon_quant rules. Should provide the option to specify these in the config file (e.g. provide a list of strings of extra parameters, then collapse into space separated string for the shell command)

SamBryce-Smith commented 1 year ago

resolved in e17dd09fba46d55762473a9f2d434f90cf775209