Typos

single_end.snakefile.smk line 235: --outSAMattrRGline ID:rcrunch SM:{params.sample_id} \, should probably be rnaseq_pipeline instead rcrunch, like it is in paired_end.snakefile.smk?
paired_end.snakefile.smk lines 172 and 176, -m 10 given twice
single_end.snakefile.smk lines 18-20. Is this really necessary? Where is this param used? Or is it missing in the shell directive?

Edited Mar 13, 2020 by BIOPZ-Katsantoni Maria

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