def run(self, config, config_file, parallel, dirs, samples):
with prun.start(_wres(parallel, ["picard"]),
samples, config, dirs, "trimming") as run_parallel:
samples = run_parallel("process_lane", samples)
samples = run_parallel("trim_lane", samples)
with prun.start(_wres(parallel, ["aligner"],
ensure_mem={"tophat": 8, "tophat2": 8, "star": 30}),
samples, config, dirs, "multicore",
multiplier=alignprep.parallel_multiplier(samples)) as run_parallel:
samples = disambiguate.split(samples)
samples = run_parallel("process_alignment", samples)
samples = disambiguate.resolve(samples, run_parallel)
with prun.start(_wres(parallel, ["samtools", "cufflinks"]),
samples, config, dirs, "rnaseqcount") as run_parallel:
samples = rnaseq.estimate_expression(samples, run_parallel)
#samples = rnaseq.detect_fusion(samples, run_parallel)
combined = combine_count_files([x[0].get("count_file") for x in samples])
gtf_file = utils.get_in(samples[0][0], ('genome_resources', 'rnaseq',
'transcripts'), None)
annotated = annotate_combined_count_file(combined, gtf_file)
for x in samples:
x[0]["combined_counts"] = combined
if annotated:
x[0]["annotated_combined_counts"] = annotated
with prun.start(_wres(parallel, ["picard", "fastqc", "rnaseqc"]),
samples, config, dirs, "persample") as run_parallel:
samples = qcsummary.generate_parallel(samples, run_parallel)
return samples
def run(self, config, config_file, parallel, dirs, samples):
with prun.start(parallel, samples, config, dirs, "trimming") as run_parallel:
samples = run_parallel("trim_lane", samples)
with prun.start(
_wprogs(parallel, ["aligner"], {"tophat": 8, "tophat2": 8, "star": 30}),
samples,
config,
dirs,
"multicore",
multiplier=alignprep.parallel_multiplier(samples),
) as run_parallel:
samples = disambiguate.split(samples)
samples = run_parallel("process_alignment", samples)
samples = disambiguate.resolve(samples, run_parallel)
with prun.start(
_wprogs(parallel, ["samtools", "gatk", "cufflinks"]), samples, config, dirs, "rnaseqcount"
) as run_parallel:
samples = rnaseq.estimate_expression(samples, run_parallel)
# samples = rnaseq.detect_fusion(samples, run_parallel)
combined = combine_count_files([x[0].get("count_file") for x in samples])
organism = utils.get_in(samples[0][0], ("genome_resources", "aliases", "ensembl"), None)
annotated = annotate_combined_count_file(combined, organism)
for x in samples:
x[0]["combined_counts"] = combined
x[0]["annotated_combined_counts"] = annotated
with prun.start(
_wprogs(parallel, ["picard", "fastqc", "rnaseqc"]), samples, config, dirs, "persample"
) as run_parallel:
samples = qcsummary.generate_parallel(samples, run_parallel)
return samples
def run(self, config, config_file, parallel, dirs, samples):
with prun.start(_wres(parallel, ["picard", "AlienTrimmer"]),
samples, config, dirs, "trimming") as run_parallel:
with profile.report("adapter trimming", dirs):
samples = run_parallel("prepare_sample", samples)
samples = run_parallel("trim_sample", samples)
with prun.start(_wres(parallel, ["aligner", "picard"],
ensure_mem={"tophat": 8, "tophat2": 8, "star": 40}),
samples, config, dirs, "multicore",
multiplier=alignprep.parallel_multiplier(samples)) as run_parallel:
with profile.report("alignment", dirs):
samples = disambiguate.split(samples)
samples = run_parallel("process_alignment", samples)
with prun.start(_wres(parallel, ["samtools", "cufflinks"]),
samples, config, dirs, "rnaseqcount") as run_parallel:
with profile.report("disambiguation", dirs):
samples = disambiguate.resolve(samples, run_parallel)
with profile.report("transcript assembly", dirs):
samples = rnaseq.assemble_transcripts(run_parallel, samples)
with profile.report("estimate expression", dirs):
samples = rnaseq.estimate_expression(samples, run_parallel)
with prun.start(_wres(parallel, ["picard", "fastqc", "rnaseqc","kraken"]),
samples, config, dirs, "persample") as run_parallel:
with profile.report("quality control", dirs):
samples = qcsummary.generate_parallel(samples, run_parallel)
logger.info("Timing: finished")
return samples
def run(self, config, run_info_yaml, parallel, dirs, samples):
with prun.start(_wres(parallel, ["aligner"],
ensure_mem={"tophat": 8, "tophat2": 8, "star": 2}),
[samples[0]], config, dirs, "organize_samples") as run_parallel:
with profile.report("organize samples", dirs):
samples = run_parallel("organize_samples", [[dirs, config, run_info_yaml,
[x[0]["description"] for x in samples]]])
with prun.start(_wres(parallel, ["picard", "cutadapt"]),
samples, config, dirs, "trimming") as run_parallel:
with profile.report("adapter trimming", dirs):
samples = run_parallel("prepare_sample", samples)
samples = run_parallel("trim_sample", samples)
with prun.start(_wres(parallel, ["aligner", "picard"],
ensure_mem={"tophat": 8, "tophat2": 8, "star": 2}),
samples, config, dirs, "alignment",
multiplier=alignprep.parallel_multiplier(samples)) as run_parallel:
with profile.report("alignment", dirs):
samples = disambiguate.split(samples)
samples = run_parallel("process_alignment", samples)
with prun.start(_wres(parallel, ["samtools", "cufflinks"]),
samples, config, dirs, "rnaseqcount") as run_parallel:
with profile.report("disambiguation", dirs):
samples = disambiguate.resolve(samples, run_parallel)
with profile.report("transcript assembly", dirs):
samples = rnaseq.assemble_transcripts(run_parallel, samples)
with profile.report("estimate expression", dirs):
samples = rnaseq.estimate_expression(samples, run_parallel)
with prun.start(_wres(parallel, ["picard", "fastqc", "rnaseqc", "kraken"]),
samples, config, dirs, "qc") as run_parallel:
with profile.report("quality control", dirs):
samples = qcsummary.generate_parallel(samples, run_parallel)
logger.info("Timing: finished")
return samples
def run(self, config, run_info_yaml, parallel, dirs, samples):
with prun.start(_wres(parallel, ["aligner"],
ensure_mem={"tophat": 8, "tophat2": 8, "star": 2}),
[samples[0]], config, dirs, "organize_samples") as run_parallel:
with profile.report("organize samples", dirs):
samples = run_parallel("organize_samples", [[dirs, config, run_info_yaml,
[x[0]["description"] for x in samples]]])
with prun.start(_wres(parallel, ["picard", "cutadapt"]),
samples, config, dirs, "trimming") as run_parallel:
with profile.report("adapter trimming", dirs):
samples = run_parallel("prepare_sample", samples)
samples = run_parallel("trim_sample", samples)
with prun.start(_wres(parallel, ["aligner", "picard"],
ensure_mem={"tophat": 8, "tophat2": 8, "star": 2}),
samples, config, dirs, "alignment",
multiplier=alignprep.parallel_multiplier(samples)) as run_parallel:
with profile.report("alignment", dirs):
samples = run_parallel("disambiguate_split", [samples])
samples = run_parallel("process_alignment", samples)
with prun.start(_wres(parallel, ["samtools", "cufflinks"]),
samples, config, dirs, "rnaseqcount") as run_parallel:
with profile.report("disambiguation", dirs):
samples = disambiguate.resolve(samples, run_parallel)
with profile.report("transcript assembly", dirs):
samples = rnaseq.assemble_transcripts(run_parallel, samples)
with profile.report("estimate expression", dirs):
samples = rnaseq.estimate_expression(samples, run_parallel)
with prun.start(_wres(parallel, ["picard", "fastqc", "rnaseqc", "kraken"]),
samples, config, dirs, "qc") as run_parallel:
with profile.report("quality control", dirs):
samples = qcsummary.generate_parallel(samples, run_parallel)
logger.info("Timing: finished")
return samples
def run(self, config, config_file, run_parallel, parallel, dirs, lane_items):
lane_items = run_parallel("trim_lane", lane_items)
samples = disambiguate.split(lane_items)
samples = run_parallel("process_alignment", samples)
samples = disambiguate.resolve(samples, run_parallel)
samples = rnaseq.estimate_expression(samples, run_parallel)
combined = combine_count_files([x[0].get("count_file") for x in samples])
for x in samples:
x[0]["combined_counts"] = combined
samples = qcsummary.generate_parallel(samples, run_parallel)
#run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
return samples
def run(self, config, config_file, parallel, dirs, samples):
with prun.start(_wres(parallel, ["picard", "AlienTrimmer"]), samples,
config, dirs, "trimming") as run_parallel:
with profile.report("adapter trimming", dirs):
samples = run_parallel("process_lane", samples)
samples = run_parallel("trim_lane", samples)
with prun.start(_wres(parallel, ["aligner", "picard"],
ensure_mem={
"tophat": 8,
"tophat2": 8,
"star": 40
}),
samples,
config,
dirs,
"multicore",
multiplier=alignprep.parallel_multiplier(
samples)) as run_parallel:
with profile.report("alignment", dirs):
samples = disambiguate.split(samples)
samples = run_parallel("process_alignment", samples)
with prun.start(_wres(parallel, ["samtools", "cufflinks"]), samples,
config, dirs, "rnaseqcount") as run_parallel:
with profile.report("disambiguation", dirs):
samples = disambiguate.resolve(samples, run_parallel)
with profile.report("estimate expression", dirs):
samples = rnaseq.estimate_expression(samples, run_parallel)
combined = combine_count_files(
[x[0].get("count_file") for x in samples])
gtf_file = utils.get_in(samples[0][0],
('genome_resources', 'rnaseq', 'transcripts'),
None)
annotated = annotate_combined_count_file(combined, gtf_file)
for x in samples:
x[0]["combined_counts"] = combined
if annotated:
x[0]["annotated_combined_counts"] = annotated
with prun.start(_wres(parallel, ["picard", "fastqc", "rnaseqc"]),
samples, config, dirs, "persample") as run_parallel:
with profile.report("quality control", dirs):
samples = qcsummary.generate_parallel(samples, run_parallel)
logger.info("Timing: finished")
return samples
def run(self, config, config_file, run_parallel, parallel, dirs, lane_items):
lane_items = run_parallel("trim_lane", lane_items)
samples = disambiguate.split(lane_items)
samples = run_parallel("process_alignment", samples)
samples = disambiguate.resolve(samples, run_parallel)
samples = rnaseq.estimate_expression(samples, run_parallel)
#samples = rnaseq.detect_fusion(samples, run_parallel)
combined = combine_count_files([x[0].get("count_file") for x in samples])
organism = utils.get_in(samples[0][0], ('genome_resources', 'aliases',
'ensembl'), None)
annotated = annotate_combined_count_file(combined, organism)
for x in samples:
x[0]["combined_counts"] = combined
x[0]["annotated_combined_counts"] = annotated
samples = qcsummary.generate_parallel(samples, run_parallel)
#run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
return samples