comparison Snakefile @ 14:f2258de365ee draft

Uploaded

13:af1f49e5242d

         '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'])
config['temp']=os.path.abspath(config['temp'])

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

rule bamcount:
    input:
        bam=config['temp'] + '/{quad}-sorted.bam',
        bamidx=config['temp'] + '/{quad}-sorted.bam.bai',
        #exe='/bamcount/bamcount',
        exe='bamcount',
        bed=lambda wildcards: '%s/%s/gtf/%s' % (config['ref'], wildcards.quad.split('_')[2], config.get('bw_bed', 'exons.bed'))
    output:
        nonref=config['output'] + '/{quad}.bamcount_nonref.csv.zst',
        auc=config['output'] + '/{quad}.bamcount_auc.tsv',
        frag=config['output'] + '/{quad}.bamcount_frag.tsv',

        uniq_qual=config.get('unique_qual', 10)
    threads: 4
    shell:
        """
        TMP={config[temp]}/{params.srr}_bamcount
        {input.exe} {input.bam} \
            --threads {threads} \
            --coverage \
            --no-head \
            --require-mdz \
            --min-unique-qual {params.uniq_qual} \

14:f2258de365ee

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

#get rid of the pesky warnings about current paths
#and make sure we're not assuming any wrong relative paths
import os
config['output']=os.path.abspath(config['output'])
config['temp']=os.path.abspath(config['temp'])
config['exon_bed']=os.path.abspath(config['exon_bed'])
config['ref']=os.path.abspath(config['ref'])

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

rule bamcount:
    input:
        bam=config['temp'] + '/{quad}-sorted.bam',
        bamidx=config['temp'] + '/{quad}-sorted.bam.bai',
        bed=lambda wildcards: '%s/%s/gtf/%s' % (config['ref'], wildcards.quad.split('_')[2], config.get('bw_bed', 'exons.bed'))
    output:
        nonref=config['output'] + '/{quad}.bamcount_nonref.csv.zst',
        auc=config['output'] + '/{quad}.bamcount_auc.tsv',
        frag=config['output'] + '/{quad}.bamcount_frag.tsv',

        uniq_qual=config.get('unique_qual', 10)
    threads: 4
    shell:
        """
        TMP={config[temp]}/{params.srr}_bamcount
        bamcount {input.bam} \
            --threads {threads} \
            --coverage \
            --no-head \
            --require-mdz \
            --min-unique-qual {params.uniq_qual} \