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thkuo / seq2geno

Computational pipeline for genomic features of bacterial population
GNU General Public License v3.0
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flexible about reads layout #40

Closed thkuo closed 6 years ago

thkuo commented 6 years ago

Automatically detect mate-pair, paired-end, and single reads and set proper options (ie. for mapping). Consequently, the script (snakemake rules) should also be able to conditionally set the command

thkuo commented 6 years ago

Implemented with rules of "switch" that decides whether to use the single or paired end mapping at the DAG stage of snakemake.