comparison Snakefile @ 11:35ed7314038d draft

Uploaded

10:f43dd6f7c687

        sys.stderr.write("error in run_command for command: %s\n" % cmd_args)
        raise cpe


import re
FASTQ_PATT=re.compile(r'([^_\.]+)_(\d+)\.((fastq)|fq)(\.gz)?$')
import os
def prep_for_galaxy_run():
    try:
        os.mkdir(config['temp'])
    except OSError as ose:
        pass
    fastqs = config['inputs'].split(',')
    m = FASTQ_PATT.search(fastqs[0])
    run_acc = m.group(1)
    study_acc = run_acc
    if 'study' in config:
        study_acc = config['study']
    genome = 'hg38'
    if 'genome' in config:

11:35ed7314038d

        sys.stderr.write("error in run_command for command: %s\n" % cmd_args)
        raise cpe


import re
FASTQ_PATT=re.compile(r'([^_\.]+)(_(\d+))?\.((fastq)|fq)(\.gz)?$')
import os
def prep_for_galaxy_run():
    try:
        os.mkdir(config['temp'])
    except OSError as ose:
        pass
    fastqs = config['inputs'].split(',')
    m = FASTQ_PATT.search(fastqs[0])
    run_acc = 'sample'
    if m is not None:
        run_acc = m.group(1)
    study_acc = run_acc
    if 'study' in config:
        study_acc = config['study']
    genome = 'hg38'
    if 'genome' in config: