def runfn(*args):
args = ipython.unzip_args(args)
assert len(args) == 1
fn_args = args[0][4:]
with _setup_logging(fn_args):
fn_name = args[0][0]
dockerconf = args[0][1]
cmd_args = args[0][2]
parallel = args[0][3]
return ipython.zip_args(run.do_runfn(fn_name, fn_args, cmd_args, parallel, dockerconf))
def run_stringtie_expression(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(rnaseq.run_stringtie_expression, *args))
def prep_align_inputs(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(alignprep.create_inputs, *args))
def cufflinks_merge(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(rnaseq.cufflinks_merge, *args))
def machine_info(*args):
args = ipython.unzip_args(args)
return ipython.zip_args(system.machine_info())
def compare_to_rm(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(validate.compare_to_rm, *args))
def merge_variant_files(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(vcfutils.merge_variant_files, *args))
def run_dexseq(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(rnaseq.run_dexseq, *args))
def merge_variant_files(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(vcfutils.merge_variant_files, *args))
def variantcall_sample(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(genotype.variantcall_sample, *args))
def combine_sample_regions(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(callable.combine_sample_regions, *args))
def combine_bam(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(shared.combine_bam, *args))
def run_dexseq(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(rnaseq.run_dexseq, *args))
def run_rnaseq_joint_genotyping(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(rnaseq.run_rnaseq_joint_genotyping, *args))
def run_rnaseq_variant_calling(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(rnaseq.run_rnaseq_variant_calling, *args))
def qsignature_summary(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(qcsummary.qsignature_summary, *args))
def run_cufflinks(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(rnaseq.run_cufflinks, *args))
def prep_gemini_db(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(population.prep_gemini_db, *args))
def combine_sample_regions(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(callable.combine_sample_regions, *args))
def call_hla(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(hla.call_hla, *args))
def detect_sv(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(structural.detect_sv, *args))
def finalize_sv(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(structural.finalize_sv, *args))
def run_disambiguate(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(disambiguate.run, *args))
def heterogeneity_estimate(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(heterogeneity.estimate, *args))
def archive_to_cram(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(archive.to_cram, *args))
def combine_calls(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(ensemble.combine_calls, *args))
def wrapper(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(fn(*args))
def compare_to_rm(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(validate.compare_to_rm, *args))
def prep_samples(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(sample.prep_samples, *args))
def run_disambiguate(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(disambiguate.run, *args))
def pipeline_summary(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(qcsummary.pipeline_summary, *args))
def disambiguate_split(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(disambiguate.split, *args))
def generate_transcript_counts(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(rnaseq.generate_transcript_counts, *args))
def disambiguate_merge_extras(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(disambiguate.merge_extras, *args))
def run_rnaseq_variant_calling(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(rnaseq.run_rnaseq_variant_calling, *args))
def machine_info(*args):
args = ipython.unzip_args(args)
return ipython.zip_args(system.machine_info())
def combine_bam(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(shared.combine_bam, *args))
def clean_chipseq_alignment(*args):
args = ipython.unzip_args(args)
return ipython.zip_args(apply(chipseq.clean_chipseq_alignment, *args))
def variantcall_sample(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(genotype.variantcall_sample, *args))
def archive_to_cram(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(archive.to_cram, *args))
def prep_gemini_db(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(population.prep_gemini_db, *args))
def square_batch_region(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(joint.square_batch_region, *args))
def combine_calls(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(ensemble.combine_calls, *args))
def cufflinks_merge(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(rnaseq.cufflinks_merge, *args))
def coverage_summary(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(coverage.summary, *args))
def stringtie_merge(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(rnaseq.stringtie_merge, *args))
def disambiguate_split(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(disambiguate.split, *args))
def organize_samples(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(run_info.organize, *args))
def clean_chipseq_alignment(*args):
args = ipython.unzip_args(args)
return ipython.zip_args(chipseq.machine_info())
def prep_system(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(run_info.prep_system, *args))
def square_batch_region(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(joint.square_batch_region, *args))
def upload_samples_project(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(upload.project_from_sample, *args))
def organize_samples(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(run_info.organize, *args))
def wrapper(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(fn(*args))
def run_sailfish(*args):
args = ipython.unzip_args(args)
with _setup_logging(args):
return ipython.zip_args(apply(sailfish.run_sailfish, *args))
def prepare_bcbio_samples(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(sample.prepare_bcbio_samples, *args))
def postprocess_alignment(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(sample.postprocess_alignment, *args))
def trim_srna_sample(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(srna.trim_srna_sample, *args))
def merge_sample(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(sample.merge_sample, *args))
def run_cufflinks(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(rnaseq.run_cufflinks, *args))