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
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
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
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