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 split_variants_by_sample(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(multi.split_variants_by_sample, *args),
config)
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 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),
config)
def combine_bam(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(shared.combine_bam, *args), config)
def run_cufflinks(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(rnaseq.run_cufflinks, *args), config)
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), config)
def pipeline_summary(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(qcsummary.pipeline_summary, *args),
config)
def postprocess_variants(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(variation.postprocess_variants, *args),
config)
def piped_bamprep(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(bamprep.piped_bamprep, *args), config)
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 variantcall_sample(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(genotype.variantcall_sample, *args),
config)
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 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),
config)
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 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),
config)
def run_disambiguate(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(disambiguate.run, *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), config)
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), config)
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), config)
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 coverage_summary(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(coverage.summary, *args), config)
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 run_disambiguate(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(disambiguate.run, *args), config)
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 archive_to_cram(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(archive.to_cram, *args), config)
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 trim_lane(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(lane.trim_lane, *args), config)
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 prep_align_inputs(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(alignprep.create_inputs, *args), config)
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 postprocess_alignment(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(lane.postprocess_alignment, *args),
config)
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 merge_sample(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(sample.merge_sample, *args), config)
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 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 coverage_summary(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(coverage.summary, *args))
def srna_annotation(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(srna.sample_annotation, *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 seqcluster_cluster(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(seqcluster.run_cluster, *args))
def clean_chipseq_alignment(*args):
args = ipython.unzip_args(args)
return ipython.zip_args(chipseq.machine_info())
def srna_alignment(* args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(seqcluster.run_align, *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 peakcalling(* args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(peaks.calling, *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 run_kallisto_rnaseq(*args):
args = ipython.unzip_args(args)
with _setup_logging(args):
return ipython.zip_args(apply(kallisto.run_kallisto_rnaseq, *args))
def run_sailfish(*args):
args = ipython.unzip_args(args)
with _setup_logging(args):
return ipython.zip_args(apply(sailfish.run_sailfish, *args))
def run_counts_spikein(*args):
args = ipython.unzip_args(args)
with _setup_logging(args):
return ipython.zip_args(apply(spikein.run_counts_spikein, *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 run_sailfish_index(*args):
args = ipython.unzip_args(args)
with _setup_logging(args):
return ipython.zip_args(apply(sailfish.run_sailfish_index, *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 prep_recal(*args):
args = ipython.unzip_args(args)
with _setup_logging(args) as config:
return ipython.zip_args(apply(recalibrate.prep_recal, *args), config)