Move run specific parameters from samples.tsv to rule_config.yaml

The current layout of ZARP requires several parameters to be specified in the samples.tsv file, that should rather be specified in the recently introduced rule_config.yaml as they apply to all samples of a run.

Necessary changes in

Snakefile, single/paired-end Snakefile
rule_config.yaml
samples.tsv, and consequently ZARP-cli. Corresponding issue here

Suggestions from #155 (closed) :
single_end.snakefile.smk and paired_end.snakefile.smk:

map_genome_star: -- twopassMode
map_genome_star: --alignEndsType

Edited Aug 20, 2021 by BIOPZ-Katsantoni Maria

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