comparison Snakefile @ 37:5656cfea6d97 draft

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36:ad4b5855143b

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

import re
#limit the outputs/steps to only 1) STAR called junctions 2) all reads per-base coverage (BigWigs) 3) all reads exon summarized coverage 4) AUC (for QC)
STEPS_FILES_FILTER=re.compile(r'(unmapped)|(download)|(salmon)|(extract_jx)|(jx_bed)|(manifest)|(nonref)|(Chimeric)(fastq_check)|(frag)|(unique)')
def remove_steps_files():
    #modify STEP and FILES
    #so we don't run download or unmapped steps
    global FILES
    global STEPS

37:5656cfea6d97

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

import re
#limit the outputs/steps to only 1) STAR called junctions 2) all reads per-base coverage (BigWigs) 3) all reads exon summarized coverage 4) AUC (for QC)
STEPS_FILES_FILTER=re.compile(r'(unmapped)|(download)|(salmon)|(extract_jx)|(jx_bed)|(manifest)|(nonref)|(Chimeric)|(fastq_check)|(frag)|(unique)')
def remove_steps_files():
    #modify STEP and FILES
    #so we don't run download or unmapped steps
    global FILES
    global STEPS