Пример #1
0
 def run(self, config, config_file, run_parallel, parallel, dirs, lane_items):
     lane_items = run_parallel("trim_lane", lane_items)
     samples = run_parallel("process_alignment", lane_items)
     samples = run_parallel("generate_transcript_counts", samples)
     samples = qcsummary.generate_parallel(samples, run_parallel)
     samples = qc.sample_summary(samples)
     #run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
     return samples
Пример #2
0
 def run(self, config, config_file, run_parallel, parallel, dirs,
         lane_items):
     lane_items = run_parallel("trim_lane", lane_items)
     samples = run_parallel("process_alignment", lane_items)
     samples = run_parallel("generate_transcript_counts", samples)
     samples = qcsummary.generate_parallel(samples, run_parallel)
     samples = qc.sample_summary(samples)
     #run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
     return samples
Пример #3
0
 def run(self, config, config_file, run_parallel, parallel, dirs, lane_items):
     lane_items = run_parallel("trim_lane", lane_items)
     align_items = run_parallel("process_alignment", lane_items)
     # process samples, potentially multiplexed across multiple lanes
     samples = organize_samples(align_items, dirs, config_file)
     samples = run_parallel("merge_sample", samples)
     samples = run_parallel("generate_transcript_counts", samples)
     samples = qcsummary.generate_parallel(samples, run_parallel)
     samples = qc.sample_summary(samples)
     #run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
     return samples
Пример #4
0
 def run(self, config, config_file, run_parallel, parallel, dirs,
         lane_items):
     lane_items = run_parallel("trim_lane", lane_items)
     align_items = run_parallel("process_alignment", lane_items)
     # process samples, potentially multiplexed across multiple lanes
     samples = organize_samples(align_items, dirs, config_file)
     samples = run_parallel("merge_sample", samples)
     samples = run_parallel("generate_transcript_counts", samples)
     samples = qcsummary.generate_parallel(samples, run_parallel)
     samples = qc.sample_summary(samples)
     #run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
     return samples