comparison Snakefile @ 12:849ab444b4f1 draft

Uploaded

11:35ed7314038d

         'bamcount_auc.tsv',
         'bamcount_frag.tsv',
         'Chimeric.out.junction.zst',
         'all.exon_bw_count.zst', 'unique.exon_bw_count.zst',
         'manifest']

import subprocess
def run_command(cmd_args):
    cmd_args = ' '.join(cmd_args)
    try:

        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:
        genome = config['genome']

12:849ab444b4f1

         'bamcount_auc.tsv',
         'bamcount_frag.tsv',
         'Chimeric.out.junction.zst',
         'all.exon_bw_count.zst', 'unique.exon_bw_count.zst',
         'manifest']

import os
config['output']=os.path.abspath(config['output'])

import subprocess
def run_command(cmd_args):
    cmd_args = ' '.join(cmd_args)
    try:

        raise cpe


import re
FASTQ_PATT=re.compile(r'([^_\.]+)(_(\d+))?\.((fastq)|fq)(\.gz)?$')
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 = 'study'
    if 'study' in config:
        study_acc = config['study']
    genome = 'hg38'
    if 'genome' in config:
        genome = config['genome']