Mercurial > repos > chrisw > monorail_test

comparison Snakefile @ 35:e4dc3d0c31de draft

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Uploaded
author chrisw
date Wed, 20 Nov 2019 00:44:24 +0000
parents 13df910d0683
children 5656cfea6d97
comparison
equal deleted inserted replaced
34:358a1cf83b7b 35:e4dc3d0c31de
44 except subprocess.CalledProcessError as cpe: 44 except subprocess.CalledProcessError as cpe:
45 sys.stderr.write("error in run_command for command: %s\n" % cmd_args) 45 sys.stderr.write("error in run_command for command: %s\n" % cmd_args)
46 raise cpe 46 raise cpe
47 47
48 import re 48 import re
49 STEPS_FILES_FILTER=re.compile(r'(unmapped)|(download)|(salmon)|(extract_jx)|(jx_bed)|(manifest)|(nonref)|(Chimeric)') 49 #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)
50 STEPS_FILES_FILTER=re.compile(r'(unmapped)|(download)|(salmon)|(extract_jx)|(jx_bed)|(manifest)|(nonref)|(Chimeric)(fastq_check)|(frag)|(unique)')
50 def remove_steps_files(): 51 def remove_steps_files():
51 #modify STEP and FILES 52 #modify STEP and FILES
52 #so we don't run download or unmapped steps 53 #so we don't run download or unmapped steps
53 global FILES 54 global FILES
54 global STEPS 55 global STEPS
173 return a 174 return a
174 175
175 rule make_galaxy_links: 176 rule make_galaxy_links:
176 input: 177 input:
177 config['output'] + '/{quad}.sjout.zst', 178 config['output'] + '/{quad}.sjout.zst',
178 config['output'] + '/{quad}.fastq_check.tsv.zst', 179 #config['output'] + '/{quad}.fastq_check.tsv.zst',
179 config['output'] + '/{quad}.bamcount_auc.tsv', 180 config['output'] + '/{quad}.bamcount_auc.tsv',
180 config['output'] + '/{quad}.bamcount_frag.tsv', 181 #config['output'] + '/{quad}.bamcount_frag.tsv',
181 config['output'] + '/{quad}.all.exon_bw_count.zst', 182 config['output'] + '/{quad}.all.exon_bw_count.zst',
182 config['output'] + '/{quad}.unique.exon_bw_count.zst', 183 #config['output'] + '/{quad}.unique.exon_bw_count.zst',
183 config['output'] + '/{quad}.all.bw.zst', 184 config['output'] + '/{quad}.all.bw.zst',
184 config['output'] + '/{quad}.unique.bw.zst', 185 #config['output'] + '/{quad}.unique.bw.zst',
185 config['output'] + '/{quad}.fastq_check.log', 186 #config['output'] + '/{quad}.fastq_check.log',
186 config['output'] + '/{quad}.align.log', 187 #config['output'] + '/{quad}.align.log',
187 config['output'] + '/{quad}.sort.log', 188 #config['output'] + '/{quad}.sort.log',
188 config['output'] + '/{quad}.bamcount.log', 189 #config['output'] + '/{quad}.bamcount.log',
189 output: 190 output:
190 config['output'] + '/{quad}.done' 191 config['output'] + '/{quad}.done'
191 params: 192 params:
192 quad=lambda wildcards: wildcards.quad, 193 quad=lambda wildcards: wildcards.quad,
193 out=galaxy_link_files(config['output']) 194 out=galaxy_link_files(config['output'])