Working Preseq

[MediciPrime]

In addition the 4C bash script has been made strict to avoid not catching errors.

[daler]

I think a cleaner way of calling these tools from snakemake would be:

rule preseq:
    input: '{sample}.bam'
    output: '{sample}.complexity'
    wrapper:
        'path/to/preseq/observed_complexity'

I can't think of a reason to ever use BED input. If we specify that the wrapper only takes BAM input, you can add the -B directly to the calls, and put -o directly into the calls as well, and not have to worry about any parameters.