def rnaseq_variant_calling(samples, run_parallel):
"""
run RNA-seq variant calling using GATK
"""
samples = run_parallel("run_rnaseq_variant_calling", samples)
variantcaller = dd.get_variantcaller(to_single_data(samples[0]))
if variantcaller and ("gatk-haplotype" in variantcaller):
out = []
for d in joint.square_off(samples, run_parallel):
out.extend(
[[to_single_data(xs)]
for xs in multi.split_variants_by_sample(to_single_data(d))])
samples = out
if variantcaller:
samples = run_parallel("run_rnaseq_ann_filter", samples)
if variantcaller and ("gatk-haplotype" in variantcaller):
out = []
for data in (to_single_data(xs) for xs in samples):
if "variants" not in data:
data["variants"] = []
data["variants"].append({
"variantcaller": "gatk-haplotype",
"vcf": data["vrn_file_orig"],
"population": {
"vcf": data["vrn_file"]
}
})
data["vrn_file"] = data.pop("vrn_file_orig")
out.append([data])
samples = out
return samples
def run(self, config, config_file, parallel, dirs, samples):
## Alignment and preparation requiring the entire input file (multicore cluster)
with prun.start(_wres(parallel, ["aligner", "samtools", "sambamba"],
(["reference", "fasta"], ["reference", "aligner"], ["files"])),
samples, config, dirs, "multicore",
multiplier=alignprep.parallel_multiplier(samples)) as run_parallel:
with profile.report("alignment preparation", dirs):
samples = run_parallel("prep_align_inputs", samples)
samples = disambiguate.split(samples)
with profile.report("alignment", dirs):
samples = run_parallel("process_alignment", samples)
samples = alignprep.merge_split_alignments(samples, run_parallel)
samples = disambiguate.resolve(samples, run_parallel)
with profile.report("callable regions", dirs):
samples = run_parallel("postprocess_alignment", samples)
samples = run_parallel("combine_sample_regions", [samples])
samples = region.clean_sample_data(samples)
with profile.report("coverage", dirs):
samples = coverage.summarize_samples(samples, run_parallel)
## Variant calling on sub-regions of the input file (full cluster)
with prun.start(_wres(parallel, ["gatk", "picard", "variantcaller"]),
samples, config, dirs, "full",
multiplier=region.get_max_counts(samples), max_multicore=1) as run_parallel:
with profile.report("alignment post-processing", dirs):
samples = region.parallel_prep_region(samples, run_parallel)
with profile.report("variant calling", dirs):
samples = genotype.parallel_variantcall_region(samples, run_parallel)
## Finalize variants (per-sample cluster)
with prun.start(_wres(parallel, ["gatk", "gatk-vqsr", "snpeff", "bcbio_variation"]),
samples, config, dirs, "persample") as run_parallel:
with profile.report("joint squaring off/backfilling", dirs):
samples = joint.square_off(samples, run_parallel)
with profile.report("variant post-processing", dirs):
samples = run_parallel("postprocess_variants", samples)
samples = run_parallel("split_variants_by_sample", samples)
with profile.report("validation", dirs):
samples = run_parallel("compare_to_rm", samples)
samples = genotype.combine_multiple_callers(samples)
## Finalizing BAMs and population databases, handle multicore computation
with prun.start(_wres(parallel, ["gemini", "samtools", "fastqc", "bamtools", "bcbio_variation",
"bcbio-variation-recall"]),
samples, config, dirs, "multicore2") as run_parallel:
with profile.report("prepped BAM merging", dirs):
samples = region.delayed_bamprep_merge(samples, run_parallel)
with profile.report("ensemble calling", dirs):
samples = ensemble.combine_calls_parallel(samples, run_parallel)
with profile.report("validation summary", dirs):
samples = validate.summarize_grading(samples)
with profile.report("structural variation", dirs):
samples = structural.run(samples, run_parallel)
with profile.report("population database", dirs):
samples = population.prep_db_parallel(samples, run_parallel)
with profile.report("quality control", dirs):
samples = qcsummary.generate_parallel(samples, run_parallel)
with profile.report("archive", dirs):
samples = archive.compress(samples, run_parallel)
logger.info("Timing: finished")
return samples
def rnaseq_variant_calling(samples, run_parallel):
"""
run RNA-seq variant calling using GATK
"""
samples = run_parallel("run_rnaseq_variant_calling", samples)
variantcaller = dd.get_variantcaller(to_single_data(samples[0]))
if variantcaller and ("gatk-haplotype" in variantcaller):
samples = joint.square_off(samples, run_parallel)
samples = run_parallel("run_rnaseq_ann_filter", samples)
return samples
def rnaseq_variant_calling(samples, run_parallel):
"""
run RNA-seq variant calling using GATK
"""
samples = run_parallel("run_rnaseq_variant_calling", samples)
variantcaller = dd.get_variantcaller(to_single_data(samples[0]))
if variantcaller and ("gatk-haplotype" in variantcaller):
out = []
for d in joint.square_off(samples, run_parallel):
out.extend([[to_single_data(xs)] for xs in multi.split_variants_by_sample(to_single_data(d))])
samples = out
samples = run_parallel("run_rnaseq_ann_filter", samples)
return samples
def rnaseq_variant_calling(samples, run_parallel):
"""
run RNA-seq variant calling using GATK
"""
samples = run_parallel("run_rnaseq_variant_calling", samples)
variantcaller = dd.get_variantcaller(to_single_data(samples[0]))
if variantcaller and ("gatk-haplotype" in variantcaller):
out = []
for d in joint.square_off(samples, run_parallel):
out.extend([[to_single_data(xs)] for xs in multi.split_variants_by_sample(to_single_data(d))])
samples = out
if variantcaller:
samples = run_parallel("run_rnaseq_ann_filter", samples)
if variantcaller and ("gatk-haplotype" in variantcaller):
out = []
for data in (to_single_data(xs) for xs in samples):
if "variants" not in data:
data["variants"] = []
data["variants"].append({"variantcaller": "gatk-haplotype", "vcf": data["vrn_file_orig"],
"population": {"vcf": data["vrn_file"]}})
data["vrn_file"] = data.pop("vrn_file_orig")
out.append([data])
samples = out
return samples
def variant2pipeline(config, run_info_yaml, parallel, dirs, samples):
## Alignment and preparation requiring the entire input file (multicore cluster)
with prun.start(
_wres(
parallel, ["aligner", "samtools", "sambamba"],
(["reference", "fasta"], ["reference", "aligner"], ["files"])),
samples,
config,
dirs,
"multicore",
multiplier=alignprep.parallel_multiplier(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]
]])
ww = initialize_watcher(samples)
with profile.report("alignment preparation", dirs):
samples = run_parallel("prep_align_inputs", samples)
ww.report("prep_align_inputs", samples)
samples = run_parallel("disambiguate_split", [samples])
with profile.report("alignment", dirs):
samples = run_parallel("process_alignment", samples)
ww.report("process_alignment", samples)
samples = disambiguate.resolve(samples, run_parallel)
samples = alignprep.merge_split_alignments(samples, run_parallel)
with profile.report("callable regions", dirs):
samples = run_parallel("prep_samples", [samples])
ww.report("prep_samples", samples)
samples = run_parallel("postprocess_alignment", samples)
ww.report("postprocess_alignment", samples)
samples = run_parallel("combine_sample_regions", [samples])
samples = region.clean_sample_data(samples)
ww.report("combine_sample_regions", samples)
with profile.report("hla typing", dirs):
samples = hla.run(samples, run_parallel)
ww.report("call_hla", samples)
## Variant calling on sub-regions of the input file (full cluster)
with prun.start(_wres(parallel, ["gatk", "picard", "variantcaller"]),
samples,
config,
dirs,
"full",
multiplier=region.get_max_counts(samples),
max_multicore=1) as run_parallel:
with profile.report("alignment post-processing", dirs):
samples = region.parallel_prep_region(samples, run_parallel)
with profile.report("variant calling", dirs):
samples = genotype.parallel_variantcall_region(
samples, run_parallel)
## Finalize variants, BAMs and population databases (per-sample multicore cluster)
with prun.start(_wres(parallel, [
"gatk", "gatk-vqsr", "snpeff", "bcbio_variation", "gemini",
"samtools", "fastqc", "sambamba", "bcbio-variation-recall",
"qsignature", "svcaller"
]),
samples,
config,
dirs,
"multicore2",
multiplier=structural.parallel_multiplier(
samples)) as run_parallel:
with profile.report("joint squaring off/backfilling", dirs):
samples = joint.square_off(samples, run_parallel)
with profile.report("variant post-processing", dirs):
samples = run_parallel("postprocess_variants", samples)
samples = run_parallel("split_variants_by_sample", samples)
with profile.report("prepped BAM merging", dirs):
samples = region.delayed_bamprep_merge(samples, run_parallel)
with profile.report("validation", dirs):
samples = run_parallel("compare_to_rm", samples)
samples = genotype.combine_multiple_callers(samples)
with profile.report("ensemble calling", dirs):
samples = ensemble.combine_calls_parallel(samples, run_parallel)
with profile.report("validation summary", dirs):
samples = validate.summarize_grading(samples)
with profile.report("structural variation precall", dirs):
samples = structural.run(samples, run_parallel, "precall")
with profile.report("structural variation", dirs):
samples = structural.run(samples, run_parallel, "initial")
with profile.report("structural variation", dirs):
samples = structural.run(samples, run_parallel, "standard")
with profile.report("structural variation ensemble", dirs):
samples = structural.run(samples, run_parallel, "ensemble")
with profile.report("structural variation validation", dirs):
samples = run_parallel("validate_sv", samples)
with profile.report("heterogeneity", dirs):
samples = heterogeneity.run(samples, run_parallel)
with profile.report("population database", dirs):
samples = population.prep_db_parallel(samples, run_parallel)
with profile.report("quality control", dirs):
ww.report("pre_qc", samples)
samples = qcsummary.generate_parallel(samples, run_parallel)
ww.report("qc_summary", samples)
with profile.report("archive", dirs):
samples = archive.compress(samples, run_parallel)
with profile.report("upload", dirs):
samples = run_parallel("upload_samples", samples)
for sample in samples:
run_parallel("upload_samples_project", [sample])
logger.info("Timing: finished")
return samples
def run(self, config, config_file, parallel, dirs, samples):
## Alignment and preparation requiring the entire input file (multicore cluster)
with prun.start(_wres(
parallel, ["aligner", "samtools", "sambamba"],
(["reference", "fasta"], ["reference", "aligner"], ["files"])),
samples,
config,
dirs,
"multicore",
multiplier=alignprep.parallel_multiplier(
samples)) as run_parallel:
with profile.report("alignment preparation", dirs):
samples = run_parallel("prep_align_inputs", samples)
samples = disambiguate.split(samples)
with profile.report("alignment", dirs):
samples = run_parallel("process_alignment", samples)
samples = alignprep.merge_split_alignments(
samples, run_parallel)
samples = disambiguate.resolve(samples, run_parallel)
with profile.report("callable regions", dirs):
samples = run_parallel("postprocess_alignment", samples)
samples = run_parallel("combine_sample_regions", [samples])
samples = region.clean_sample_data(samples)
with profile.report("coverage", dirs):
samples = coverage.summarize_samples(samples, run_parallel)
## Variant calling on sub-regions of the input file (full cluster)
with prun.start(_wres(parallel, ["gatk", "picard", "variantcaller"]),
samples,
config,
dirs,
"full",
multiplier=region.get_max_counts(samples),
max_multicore=1) as run_parallel:
with profile.report("alignment post-processing", dirs):
samples = region.parallel_prep_region(samples, run_parallel)
with profile.report("variant calling", dirs):
samples = genotype.parallel_variantcall_region(
samples, run_parallel)
## Finalize variants, BAMs and population databases (per-sample multicore cluster)
with prun.start(
_wres(parallel, [
"gatk", "gatk-vqsr", "snpeff", "bcbio_variation", "gemini",
"samtools", "fastqc", "bamtools", "bcbio-variation-recall",
"qsignature"
]), samples, config, dirs, "multicore2") as run_parallel:
with profile.report("joint squaring off/backfilling", dirs):
samples = joint.square_off(samples, run_parallel)
with profile.report("variant post-processing", dirs):
samples = run_parallel("postprocess_variants", samples)
samples = run_parallel("split_variants_by_sample", samples)
with profile.report("prepped BAM merging", dirs):
samples = region.delayed_bamprep_merge(samples, run_parallel)
with profile.report("validation", dirs):
samples = run_parallel("compare_to_rm", samples)
samples = genotype.combine_multiple_callers(samples)
with profile.report("ensemble calling", dirs):
samples = ensemble.combine_calls_parallel(
samples, run_parallel)
with profile.report("validation summary", dirs):
samples = validate.summarize_grading(samples)
with profile.report("structural variation", dirs):
samples = structural.run(samples, run_parallel)
with profile.report("population database", dirs):
samples = population.prep_db_parallel(samples, run_parallel)
with profile.report("quality control", dirs):
samples = qcsummary.generate_parallel(samples, run_parallel)
with profile.report("archive", dirs):
samples = archive.compress(samples, run_parallel)
logger.info("Timing: finished")
return samples
def variant2pipeline(config, run_info_yaml, parallel, dirs, samples):
## Alignment and preparation requiring the entire input file (multicore cluster)
with prun.start(_wres(parallel, ["aligner", "samtools", "sambamba"],
(["reference", "fasta"], ["reference", "aligner"], ["files"])),
samples, config, dirs, "multicore",
multiplier=alignprep.parallel_multiplier(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]]])
ww = WorldWatcher(dirs["work"], is_on=any([dd.get_cwl_reporting(d[0]) for d in samples]))
ww.initialize(samples)
with profile.report("alignment preparation", dirs):
samples = run_parallel("prep_align_inputs", samples)
ww.report("prep_align_inputs", samples)
samples = run_parallel("disambiguate_split", [samples])
with profile.report("alignment", dirs):
samples = run_parallel("process_alignment", samples)
ww.report("process_alignment", samples)
samples = disambiguate.resolve(samples, run_parallel)
samples = alignprep.merge_split_alignments(samples, run_parallel)
with profile.report("callable regions", dirs):
samples = run_parallel("prep_samples", [samples])
ww.report("prep_samples", samples)
samples = run_parallel("postprocess_alignment", samples)
ww.report("postprocess_alignment", samples)
samples = run_parallel("combine_sample_regions", [samples])
samples = region.clean_sample_data(samples)
ww.report("combine_sample_regions", samples)
with profile.report("structural variation initial", dirs):
samples = structural.run(samples, run_parallel, "initial")
ww.report("sv_initial", samples)
with profile.report("hla typing", dirs):
samples = hla.run(samples, run_parallel)
ww.report("call_hla", samples)
## Variant calling on sub-regions of the input file (full cluster)
with prun.start(_wres(parallel, ["gatk", "picard", "variantcaller"]),
samples, config, dirs, "full",
multiplier=region.get_max_counts(samples), max_multicore=1) as run_parallel:
with profile.report("alignment post-processing", dirs):
samples = region.parallel_prep_region(samples, run_parallel)
with profile.report("variant calling", dirs):
samples = genotype.parallel_variantcall_region(samples, run_parallel)
## Finalize variants, BAMs and population databases (per-sample multicore cluster)
with prun.start(_wres(parallel, ["gatk", "gatk-vqsr", "snpeff", "bcbio_variation",
"gemini", "samtools", "fastqc", "bamtools",
"bcbio-variation-recall", "qsignature",
"svcaller"]),
samples, config, dirs, "multicore2",
multiplier=structural.parallel_multiplier(samples)) as run_parallel:
with profile.report("joint squaring off/backfilling", dirs):
samples = joint.square_off(samples, run_parallel)
with profile.report("variant post-processing", dirs):
samples = run_parallel("postprocess_variants", samples)
samples = run_parallel("split_variants_by_sample", samples)
with profile.report("prepped BAM merging", dirs):
samples = region.delayed_bamprep_merge(samples, run_parallel)
with profile.report("validation", dirs):
samples = run_parallel("compare_to_rm", samples)
samples = genotype.combine_multiple_callers(samples)
with profile.report("ensemble calling", dirs):
samples = ensemble.combine_calls_parallel(samples, run_parallel)
with profile.report("validation summary", dirs):
samples = validate.summarize_grading(samples)
with profile.report("structural variation final", dirs):
samples = structural.run(samples, run_parallel, "standard")
with profile.report("structural variation ensemble", dirs):
samples = structural.run(samples, run_parallel, "ensemble")
with profile.report("structural variation validation", dirs):
samples = run_parallel("validate_sv", samples)
with profile.report("heterogeneity", dirs):
samples = heterogeneity.run(samples, run_parallel)
with profile.report("population database", dirs):
samples = population.prep_db_parallel(samples, run_parallel)
with profile.report("quality control", dirs):
ww.report("pre_qc", samples)
samples = qcsummary.generate_parallel(samples, run_parallel)
ww.report("qc_summary", samples)
with profile.report("archive", dirs):
samples = archive.compress(samples, run_parallel)
with profile.report("upload", dirs):
samples = run_parallel("upload_samples", samples)
for sample in samples:
run_parallel("upload_samples_project", [sample])
logger.info("Timing: finished")
return samples