Restructuring the tool parameter specification within rules to allow for more parameters to be changed.

Discussion on: https://git.scicore.unibas.ch/zavolan_group/pipelines/zarp/-/wikis/Design-discussions#passing-tool-parameters.

New design that has:

• rule congif file with additional standard parameters
• read function within Snakefile to parse this config
• Additional parameter specified within each rule that contain a string specified from parsing the rule config with the read function

As I was going through the rules, I found some examples of parameters that can be added to the additional parameters rule config, as the choices are not the defaults, but we would like the user to be able to change them.

Proposed parameters to be moved to the additional parameters:

• single_end.snakefile.smk

• remove_adapters_cutadapt: -m 10 (default=0, reads that are empty are kept)

• remove_adapters_cutadapt: -n 2 (default=1, expected occurrences of adapters)

• remove_polya_cutadapt: -O 1 (default=3, minimum overlap of the adapter , ensure that even one A in the end is trimmed, maybe user can modify if they want to be more strict or lenient with the trimming)

• remove_polya_cutadapt: -m 10 same as remove_adapters_cutadapt

• map_genome_star: -- twopassMode (currently in the samples tables, should rather be in the rule config)

• map_genome_star: -- outFilterMultimapScoreRange 0 (default 1, affects how lenient we want to be with what we consider a multi-mapper)

• map_genome_star: -- outSAMattributes All (default Standard, some extra columns are used to do transcript reconstruction eg. downstream)

• map_genome_star: --outFilterType BySJout (default Normal, the BySJout removes some spurious junctions)

• map_genome_star: --alignEndsType (currently sample specific, consider moving it to the additional)

• quantification_salmon: --seqBias (is useful to be more accurate in the salmon estimates)

• quantification_salmon: --validateMappings (is useful to be more accurate in the salmon estimates)

• paired_end.snakefile.smk

• remove_adapters_cutadapt: -m 10 (default=0, reads that are empty are kept)

• remove_adapters_cutadapt: -n 2 (default=1, expected occurrences of adapters)

• remove_polya_cutadapt: -O 1 (default=3, minimum overlap of the adapter , ensure that even one A in the end is trimmed, maybe user can modify if they want to be more strict or lenient with the trimming)

• remove_polya_cutadapt: -m 10 same as remove_adapters_cutadapt

• map_genome_star: -- twopassMode (currently in the samples tables, should rather be in the rule config)

• map_genome_star: -- outFilterMultimapScoreRange 0 (default 1, affects how lenient we want to be with what we consider a multi-mapper)

• map_genome_star: -- outSAMattributes All (default Standard, some extra columns are used to do transcript reconstruction eg. downstream)

• map_genome_star: --outFilterType BySJout (default Normal, the BySJout removes some spurious junctions)

• map_genome_star: --alignEndsType (currently sample specific, consider moving it to the additional)

• quantification_salmon: --seqBias (is useful to be more accurate in the salmon estimates)

• quantification_salmon: --validateMappings (is useful to be more accurate in the salmon estimates)

added Doing label

mentioned in merge request !83 (merged)

marked the checklist item rule congif file with additional standard parameters as completed

marked the checklist item read function within Snakefile to parse this config as completed

marked the checklist item Additional parameter specified within each rule that contain a string specified from parsing the rule config with the read function as completed

mentioned in issue #158 (closed)

removed Doing label

closed