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BIMSBbioinfo / pigx_rnaseq

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
GNU General Public License v3.0
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Adding cmd-line options for salmon via yaml doesn't work #68

Closed Nicolai-vKuegelgen closed 3 years ago

Nicolai-vKuegelgen commented 4 years ago

The "tools" section of the yaml file is supposed to allow customisation of cmd-line options, however this doesn't work properly for salmon due to 2 reasons:

1) salmon quant & salmon index use the same tool entry (whereas star_map and star_index have separate entries); most cmd options only apply to one of the two salmon usages and will fail if applied to both.

2) Compared to STAR the options for salmon need to go after the first subargument, i.e.: salmon quant {options}. To make the cmd-line options customisable with the current setup of the pipeline the quant / index part of the command needs to move from the rule definition to the executable (or args) part of the settings file.

Proposed solution:

tools:
   salmon:
    executable: @SALMON@
    args: ""

becomes: 

tools:
   salmon_index:
    executable: "@SALMON@ index"
    args: ""
  salmon_quant:
    executable: "@SALMON@ quant"
    args: ""
rekado commented 3 years ago

Thanks, Nicolai, for reporting the issue and explaining why it makes sense to split the two uses of Salmon in the settings file. It's now implemented in the master branch.