determining maximum read length should happen in a follow function

databio / peppro

A modular, containerized pipeline for PRO-seq data processing

http://peppro.databio.org/

BSD 2-Clause "Simplified" License

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determining maximum read length should happen in a follow function #37

Closed nsheff closed 4 years ago

nsheff commented 5 years ago

    # Determine maximum read length
    cmd = (tools.samtools + " stats " + mapping_genome_bam +
           " | grep '^SN' | cut -f 2- | grep 'maximum length:' | cut -f 2-")
    max_len = int(pm.checkprint(cmd))

otherwise this runs again on every re-run. it need only run right after the time that the output is produced.