def smallrnaseqpipeline(config, run_info_yaml, parallel, dirs, samples):
# causes a circular import at the top level
from bcbio.srna.group import report as srna_report
samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs,
samples)
with prun.start(
_wres(parallel, ["aligner", "picard", "samtools"],
ensure_mem={
"bowtie": 8,
"bowtie2": 8,
"star": 2
}), [samples[0]], config, dirs, "alignment") as run_parallel:
with profile.report("prepare", dirs):
samples = run_parallel("seqcluster_prepare", [samples])
with profile.report("seqcluster alignment", dirs):
samples = run_parallel("srna_alignment", [samples])
with prun.start(
_wres(parallel, ["aligner", "picard", "samtools"],
ensure_mem={
"tophat": 10,
"tophat2": 10,
"star": 2,
"hisat2": 8
}),
samples,
config,
dirs,
"alignment_samples",
multiplier=alignprep.parallel_multiplier(samples)) as run_parallel:
with profile.report("alignment", dirs):
samples = run_parallel("process_alignment", samples)
with prun.start(_wres(parallel, ["picard", "miraligner"]), samples, config,
dirs, "annotation") as run_parallel:
with profile.report("small RNA annotation", dirs):
samples = run_parallel("srna_annotation", samples)
with prun.start(
_wres(parallel, ["seqcluster", "mirge"],
ensure_mem={"seqcluster": 8}), [samples[0]], config, dirs,
"cluster") as run_parallel:
with profile.report("cluster", dirs):
samples = run_parallel("seqcluster_cluster", [samples])
with prun.start(_wres(parallel, ["picard", "fastqc"]), samples, config,
dirs, "qc") as run_parallel:
with profile.report("quality control", dirs):
samples = qcsummary.generate_parallel(samples, run_parallel)
with profile.report("report", dirs):
srna_report(samples)
with profile.report("upload", dirs):
samples = run_parallel("upload_samples", samples)
for sample in samples:
run_parallel("upload_samples_project", [sample])
return samples
def run(self, config, run_info_yaml, parallel, dirs, samples):
# causes a circular import at the top level
from bcbio.srna.group import report as srna_report
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_srna_sample", samples)
with prun.start(
_wres(parallel, ["aligner", "picard", "samtools"],
ensure_mem={
"bowtie": 8,
"bowtie2": 8,
"star": 2
}), [samples[0]], config, dirs,
"alignment") as run_parallel:
with profile.report("prepare", dirs):
samples = run_parallel("seqcluster_prepare", [samples])
with profile.report("alignment", dirs):
samples = run_parallel("srna_alignment", [samples])
with prun.start(_wres(parallel, ["picard", "miraligner"]), samples,
config, dirs, "annotation") as run_parallel:
with profile.report("small RNA annotation", dirs):
samples = run_parallel("srna_annotation", samples)
with prun.start(
_wres(parallel, ["seqcluster"], ensure_mem={"seqcluster": 8}),
[samples[0]], config, dirs, "cluster") as run_parallel:
with profile.report("cluster", dirs):
samples = run_parallel("seqcluster_cluster", [samples])
with prun.start(_wres(parallel, ["picard", "fastqc"]), samples, config,
dirs, "qc") as run_parallel:
with profile.report("quality control", dirs):
samples = qcsummary.generate_parallel(samples, run_parallel)
with profile.report("report", dirs):
srna_report(samples)
with profile.report("upload", dirs):
samples = run_parallel("upload_samples", samples)
for sample in samples:
run_parallel("upload_samples_project", [sample])
return samples
def run(self, config, run_info_yaml, parallel, dirs, samples):
# causes a circular import at the top level
from bcbio.srna.group import report as srna_report
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_srna_sample", samples)
with prun.start(_wres(parallel, ["aligner", "picard", "samtools"],
ensure_mem={"bowtie": 8, "bowtie2": 8, "star": 2}),
[samples[0]], config, dirs, "alignment") as run_parallel:
with profile.report("prepare", dirs):
samples = run_parallel("seqcluster_prepare", [samples])
with profile.report("alignment", dirs):
samples = run_parallel("srna_alignment", [samples])
with prun.start(_wres(parallel, ["picard", "miraligner"]),
samples, config, dirs, "annotation") as run_parallel:
with profile.report("small RNA annotation", dirs):
samples = run_parallel("srna_annotation", samples)
with prun.start(_wres(parallel, ["seqcluster"],
ensure_mem={"seqcluster": 8}),
[samples[0]], config, dirs, "cluster") as run_parallel:
with profile.report("cluster", dirs):
samples = run_parallel("seqcluster_cluster", [samples])
with prun.start(_wres(parallel, ["picard", "fastqc"]),
samples, config, dirs, "qc") as run_parallel:
with profile.report("quality control", dirs):
samples = qcsummary.generate_parallel(samples, run_parallel)
with profile.report("report", dirs):
srna_report(samples)
with profile.report("upload", dirs):
samples = run_parallel("upload_samples", samples)
for sample in samples:
run_parallel("upload_samples_project", [sample])
return samples
def smallrnaseqpipeline(config, run_info_yaml, parallel, dirs, samples):
# causes a circular import at the top level
from bcbio.srna.group import report as srna_report
samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples)
with prun.start(_wres(parallel, ["aligner", "picard", "samtools"],
ensure_mem={"bowtie": 8, "bowtie2": 8, "star": 2}),
[samples[0]], config, dirs, "alignment") as run_parallel:
with profile.report("prepare", dirs):
samples = run_parallel("seqcluster_prepare", [samples])
with profile.report("seqcluster alignment", dirs):
samples = run_parallel("srna_alignment", [samples])
with prun.start(_wres(parallel, ["aligner", "picard", "samtools"],
ensure_mem={"tophat": 10, "tophat2": 10, "star": 2, "hisat2": 8}),
samples, config, dirs, "alignment_samples",
multiplier=alignprep.parallel_multiplier(samples)) as run_parallel:
with profile.report("alignment", dirs):
samples = run_parallel("process_alignment", samples)
with prun.start(_wres(parallel, ["picard", "miraligner"]),
samples, config, dirs, "annotation") as run_parallel:
with profile.report("small RNA annotation", dirs):
samples = run_parallel("srna_annotation", samples)
with prun.start(_wres(parallel, ["seqcluster", "mirge"],
ensure_mem={"seqcluster": 8}),
[samples[0]], config, dirs, "cluster") as run_parallel:
with profile.report("cluster", dirs):
samples = run_parallel("seqcluster_cluster", [samples])
with prun.start(_wres(parallel, ["picard", "fastqc"]),
samples, config, dirs, "qc") as run_parallel:
with profile.report("quality control", dirs):
samples = qcsummary.generate_parallel(samples, run_parallel)
with profile.report("report", dirs):
srna_report(samples)
with profile.report("upload", dirs):
samples = run_parallel("upload_samples", samples)
for sample in samples:
run_parallel("upload_samples_project", [sample])
return samples
