comparison Snakefile @ 32:13df910d0683 draft

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31:de65ca585930

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

import re
STEPS_FILES_FILTER=re.compile(r'(unmapped)|(download)|(salmon)|(extract_jx)|(jx_bed)|(manifest)')
def remove_steps_files():
    #modify STEP and FILES
    #so we don't run download or unmapped steps
    global FILES
    global STEPS

            os.symlink(os.path.abspath(newf), '%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, 0))
        i += 1
    #create fastq 2 if not paired
    if i == 2:
        open('%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, 2), "w").close() 
    #create expected file structure for annotated exon bed file & reference index
    #ref = config['ref']
    #config['ref'] = os.path.abspath('.')
    #os.makedirs('%s/%s' % (config['ref'], genome))
    #os.symlink(ref, '%s/%s/star_idx' % (config['ref'], genome))
    #os.makedirs('%s/%s/gtf' % (config['ref'], genome))
    #os.symlink(config['exon_bed'], 'exons.tmp')
    #os.symlink('../../exons.tmp', '%s/%s/gtf/%s' % (config['ref'], genome, config.get('bw_bed', 'exons.bed')))
    #TODO may need to add additional symlinking for HISAT2 unmapped alignments
    return([run_acc, study_acc, genome, method])


def get_accessions(wildcards):
    """

rule make_galaxy_links:
    input: 
        config['output'] + '/{quad}.sjout.zst',
        config['output'] + '/{quad}.fastq_check.tsv.zst',
        config['output'] + '/{quad}.bamcount_nonref.csv.zst',
        config['output'] + '/{quad}.bamcount_auc.tsv',
        config['output'] + '/{quad}.bamcount_frag.tsv',
        config['output'] + '/{quad}.Chimeric.out.junction.zst',
        config['output'] + '/{quad}.all.exon_bw_count.zst',
        config['output'] + '/{quad}.unique.exon_bw_count.zst',
        config['output'] + '/{quad}.all.bw.zst',
        config['output'] + '/{quad}.unique.bw.zst',
        config['output'] + '/{quad}.fastq_check.log',

32:13df910d0683

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

import re
STEPS_FILES_FILTER=re.compile(r'(unmapped)|(download)|(salmon)|(extract_jx)|(jx_bed)|(manifest)|(nonref)|(Chimeric)')
def remove_steps_files():
    #modify STEP and FILES
    #so we don't run download or unmapped steps
    global FILES
    global STEPS

            os.symlink(os.path.abspath(newf), '%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, 0))
        i += 1
    #create fastq 2 if not paired
    if i == 2:
        open('%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, 2), "w").close() 
    return([run_acc, study_acc, genome, method])


def get_accessions(wildcards):
    """

rule make_galaxy_links:
    input: 
        config['output'] + '/{quad}.sjout.zst',
        config['output'] + '/{quad}.fastq_check.tsv.zst',
        config['output'] + '/{quad}.bamcount_auc.tsv',
        config['output'] + '/{quad}.bamcount_frag.tsv',
        config['output'] + '/{quad}.all.exon_bw_count.zst',
        config['output'] + '/{quad}.unique.exon_bw_count.zst',
        config['output'] + '/{quad}.all.bw.zst',
        config['output'] + '/{quad}.unique.bw.zst',
        config['output'] + '/{quad}.fastq_check.log',