Remove arguments with default setting from Snakefiles (general)

In order to increase readability of code, we should remove arguments/options that are set to the tools' default settings (and can't be changed by the user) from the shell calls within rules.

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Since we have a reasonable integration test, I think that's a great idea. If, however, we didn't have good tests, it would mean that bumping a tool's version (e.g., because of some bug/security issue) might have obscure side effects, because default values may change. Probably not a bad idea to set up another integration test with real data that we should manually run whenever we bump the version, just to make sure all of our tools still give expected results.

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changed milestone to %pipeline

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Either we interface these extra options for the user, or eliminate them. We can keep some options for STAR e.g in a separate parameter file.

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assigned to @herrmchr

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I have removed all default arguments for now, however, we should probably discuss more about how we make our choices of fixed arguments visible to the user. E.g. would it be better to retrieve ALL parameters from the config, for example by having a config template that already contains our fixed parameters. Experienced users could then change those parameters without having to change the Snakefile. Moreover, we could provide kind of a blank parameter for each tool in the config, where experienced users could specify additional parameters that we are not using by default as a string. This bears some dangers though in terms of conflicting parameters that wouldn't be checked.

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assigned to @katsanto and unassigned @herrmchr

Working on branch remove_defaults Please:

• revisit all parameters in all three Snakefiles and remove additional ones that should be default and are currently set to other values.
• Remember to change pipeline documentation accordingly.
• Deal with #152 (closed).

assigned to @herrmchr and unassigned @katsanto

Remove extra parameters:

• Snakefile
• star_rpm: --outWigNorm (default RPM was used)
• star_rpm: --outWigStrand (default Stranded was used)
• rename_star_rpm_for_alfa: orientation in params is redundant (Fixes #152 (closed))
• single_end.snakefile.smk
• map_genome_star: outFilterMismatchNoverLmax
• map_genome_star: outFilterScoreMinOverLread
• map_genome_star: outFilterMatchNminOverLread
• quantification_salmon: --writeUnmappedNames
• paired_end.snakefile.smk
• pe_map_genome_star: outFilterMismatchNoverLmax
• pe_map_genome_star: outFilterScoreMinOverLread
• pe_map_genome_star: outFilterMatchNminOverLread
• quantification_salmon: --writeUnmappedNames

assigned to @katsanto and unassigned @herrmchr

mentioned in merge request !80 (merged)

closed