def rnaseqpipeline(config, run_info_yaml, parallel, dirs, samples): samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples) with prun.start( _wres(parallel, ["aligner", "picard", "samtools"], ensure_mem={ "tophat": 10, "tophat2": 10, "star": 2, "hisat2": 8 }), 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 (threaded)", dirs): samples = rnaseq.quantitate_expression_parallel( samples, run_parallel) with prun.start(_wres(parallel, ["dexseq", "express"]), samples, config, dirs, "rnaseqcount-singlethread", max_multicore=1) as run_parallel: with profile.report("estimate expression (single threaded)", dirs): samples = rnaseq.quantitate_expression_noparallel( samples, run_parallel) samples = rnaseq.combine_files(samples) with prun.start(_wres(parallel, ["gatk", "vardict"]), samples, config, dirs, "rnaseq-variation") as run_parallel: with profile.report("RNA-seq variant calling", dirs): samples = rnaseq.rnaseq_variant_calling(samples, run_parallel) with prun.start( _wres( parallel, ["samtools", "fastqc", "qualimap", "kraken", "gatk", "preseq"], ensure_mem={"qualimap": 4}), samples, config, dirs, "qc") as run_parallel: with profile.report("quality control", dirs): samples = qcsummary.generate_parallel(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, run_info_yaml, parallel, dirs, samples): with prun.start(_wres(parallel, ["picard", "cutadapt"]), samples, config, dirs, "trimming") 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 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 (threaded)", dirs): samples = rnaseq.quantitate_expression_parallel( samples, run_parallel) with prun.start(_wres(parallel, ["dexseq", "express"]), samples, config, dirs, "rnaseqcount-singlethread", max_multicore=1) as run_parallel: with profile.report("estimate expression (single threaded)", dirs): samples = rnaseq.quantitate_expression_noparallel( samples, run_parallel) samples = rnaseq.combine_files(samples) with prun.start(_wres(parallel, ["gatk"]), samples, config, dirs, "rnaseq-variation") as run_parallel: with profile.report("RNA-seq variant calling", dirs): samples = rnaseq.rnaseq_variant_calling(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, ["picard", "cutadapt"]), samples, config, dirs, "trimming") 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 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 (threaded)", dirs): samples = rnaseq.quantitate_expression_parallel(samples, run_parallel) with prun.start( _wres(parallel, ["dexseq", "express"]), samples, config, dirs, "rnaseqcount-singlethread", max_multicore=1 ) as run_parallel: with profile.report("estimate expression (single threaded)", dirs): samples = rnaseq.quantitate_expression_noparallel(samples, run_parallel) samples = rnaseq.combine_files(samples) with prun.start(_wres(parallel, ["gatk"]), samples, config, dirs, "rnaseq-variation") as run_parallel: with profile.report("RNA-seq variant calling", dirs): samples = rnaseq.rnaseq_variant_calling(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) with profile.report("upload", dirs): for sample in samples: run_parallel("upload_samples", [sample]) logger.info("Timing: finished") return samples
def rnaseqpipeline(config, run_info_yaml, parallel, dirs, samples): samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples) with prun.start(_wres(parallel, ["aligner", "picard", "samtools"], ensure_mem={"tophat": 10, "tophat2": 10, "star": 2, "hisat2": 8}), 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 (threaded)", dirs): samples = rnaseq.quantitate_expression_parallel(samples, run_parallel) with prun.start(_wres(parallel, ["ericscript"]), samples, config, dirs, "fusion-standalone-callers") as run_parallel: with profile.report("Detect gene fusions", dirs): rnaseq.detect_fusions(samples) with prun.start(_wres(parallel, ["dexseq", "express"]), samples, config, dirs, "rnaseqcount-singlethread", max_multicore=1) as run_parallel: with profile.report("estimate expression (single threaded)", dirs): samples = rnaseq.quantitate_expression_noparallel(samples, run_parallel) samples = rnaseq.combine_files(samples) with prun.start(_wres(parallel, ["gatk"]), samples, config, dirs, "rnaseq-variation") as run_parallel: with profile.report("RNA-seq variant calling", dirs): samples = rnaseq.rnaseq_variant_calling(samples, run_parallel) with prun.start(_wres(parallel, ["samtools", "fastqc", "qualimap", "kraken", "gatk", "preseq"], ensure_mem={"qualimap": 4}), samples, config, dirs, "qc") as run_parallel: with profile.report("quality control", dirs): samples = qcsummary.generate_parallel(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 fastrnaseqpipeline(config, run_info_yaml, parallel, dirs, samples): samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples) ww = initialize_watcher(samples) with prun.start(_wres(parallel, ["samtools"]), samples, config, dirs, "fastrnaseq") as run_parallel: with profile.report("fastrnaseq", dirs): samples = rnaseq.fast_rnaseq(samples, run_parallel) ww.report("fastrnaseq", samples) samples = rnaseq.combine_files(samples) with profile.report("quality control", dirs): samples = qcsummary.generate_parallel(samples, run_parallel) ww.report("qcsummary", samples) with profile.report("upload", dirs): samples = run_parallel("upload_samples", samples) for samples in samples: run_parallel("upload_samples_project", [samples]) logger.info("Timing: finished") return samples
def rnaseqpipeline(config, run_info_yaml, parallel, dirs, samples): samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples) with prun.start( _wres(parallel, ["aligner", "picard", "samtools"], ensure_mem={ "tophat": 10, "tophat2": 10, "star": 2, "hisat2": 8 }), 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 (threaded)", dirs): samples = rnaseq.quantitate_expression_parallel( samples, run_parallel) with prun.start(_wres(parallel, ["dexseq", "express"]), samples, config, dirs, "rnaseqcount-singlethread", max_multicore=1) as run_parallel: with profile.report("estimate expression (single threaded)", dirs): samples = rnaseq.quantitate_expression_noparallel( samples, run_parallel) samples = rnaseq.combine_files(samples) with prun.start(_wres(parallel, ["gatk", "vardict"]), samples, config, dirs, "rnaseq-variation") as run_parallel: with profile.report("RNA-seq variant calling", dirs): samples = rnaseq.rnaseq_variant_calling(samples, run_parallel) with prun.start( _wres( parallel, ["samtools", "fastqc", "qualimap", "kraken", "gatk", "preseq"], ensure_mem={"qualimap": 4}), samples, config, dirs, "qc") as run_parallel: with profile.report("quality control", dirs): samples = qcsummary.generate_parallel(samples, run_parallel) with profile.report("create SummarizedExperiment object", dirs): samples = rnaseq.load_summarizedexperiment(samples) with profile.report("upload", dirs): samples = run_parallel("upload_samples", samples) for sample in samples: run_parallel("upload_samples_project", [sample]) with profile.report("bcbioRNAseq loading", dirs): tools_on = dd.get_in_samples(samples, dd.get_tools_on) bcbiornaseq_on = tools_on and "bcbiornaseq" in tools_on if bcbiornaseq_on: if len(samples) < 3: logger.warn( "bcbioRNASeq needs at least three samples total, skipping." ) elif len(samples) > 100: logger.warn("Over 100 samples, skipping bcbioRNASeq.") else: run_parallel("run_bcbiornaseqload", [sample]) logger.info("Timing: finished") return samples