HISTORY.md
LICENSE.txt
MANIFEST.in
README.rst
TODO.md
requirements-conda.txt
requirements.txt
setup.py
bcbio/__init__.py
bcbio/install.py
bcbio/utils.py
bcbio/bam/__init__.py
bcbio/bam/callable.py
bcbio/bam/counts.py
bcbio/bam/coverage.py
bcbio/bam/cram.py
bcbio/bam/fasta.py
bcbio/bam/fastq.py
bcbio/bam/ref.py
bcbio/bam/sambamba.py
bcbio/bam/skewer.py
bcbio/bam/trim.py
bcbio/bed/__init__.py
bcbio/broad/__init__.py
bcbio/broad/metrics.py
bcbio/broad/picardrun.py
bcbio/chipseq/__init__.py
bcbio/chipseq/macs2.py
bcbio/chipseq/peaks.py
bcbio/cwl/__init__.py
bcbio/cwl/create.py
bcbio/cwl/cwlutils.py
bcbio/cwl/defs.py
bcbio/cwl/inspect.py
bcbio/cwl/main.py
bcbio/cwl/tool.py
bcbio/cwl/workflow.py
bcbio/distributed/__init__.py
bcbio/distributed/clargs.py
bcbio/distributed/clusterk.py
bcbio/distributed/ipython.py
bcbio/distributed/ipythontasks.py
bcbio/distributed/multi.py
bcbio/distributed/multitasks.py
bcbio/distributed/objectstore.py
bcbio/distributed/prun.py
bcbio/distributed/resources.py
bcbio/distributed/runfn.py
bcbio/distributed/split.py
bcbio/distributed/transaction.py
bcbio/galaxy/__init__.py
bcbio/galaxy/api.py
bcbio/galaxy/loc.py
bcbio/galaxy/nglims.py
bcbio/graph/__init__.py
bcbio/graph/collectl.py
bcbio/graph/graph.py
bcbio/heterogeneity/__init__.py
bcbio/heterogeneity/bubbletree.py
bcbio/heterogeneity/chromhacks.py
bcbio/heterogeneity/phylowgs.py
bcbio/heterogeneity/theta.py
bcbio/hla/__init__.py
bcbio/hla/bwakit.py
bcbio/hla/groups.py
bcbio/hla/optitype.py
bcbio/hmmer/__init__.py
bcbio/hmmer/search.py
bcbio/illumina/__init__.py
bcbio/illumina/demultiplex.py
bcbio/illumina/flowcell.py
bcbio/illumina/machine.py
bcbio/illumina/samplesheet.py
bcbio/illumina/transfer.py
bcbio/log/__init__.py
bcbio/log/logbook_zmqpush.py
bcbio/ngsalign/__init__.py
bcbio/ngsalign/alignprep.py
bcbio/ngsalign/bowtie.py
bcbio/ngsalign/bowtie2.py
bcbio/ngsalign/bwa.py
bcbio/ngsalign/hisat2.py
bcbio/ngsalign/mosaik.py
bcbio/ngsalign/novoalign.py
bcbio/ngsalign/postalign.py
bcbio/ngsalign/rapmap.py
bcbio/ngsalign/rtg.py
bcbio/ngsalign/snap.py
bcbio/ngsalign/star.py
bcbio/ngsalign/tophat.py
bcbio/picard/__init__.py
bcbio/picard/metrics.py
bcbio/picard/utils.py
bcbio/pipeline/__init__.py
bcbio/pipeline/alignment.py
bcbio/pipeline/archive.py
bcbio/pipeline/cleanbam.py
bcbio/pipeline/config_utils.py
bcbio/pipeline/datadict.py
bcbio/pipeline/fastq.py
bcbio/pipeline/genome.py
bcbio/pipeline/main.py
bcbio/pipeline/merge.py
bcbio/pipeline/qcsummary.py
bcbio/pipeline/region.py
bcbio/pipeline/rnaseq.py
bcbio/pipeline/run_info.py
bcbio/pipeline/sample.py
bcbio/pipeline/shared.py
bcbio/pipeline/sra.py
bcbio/pipeline/tools.py
bcbio/pipeline/variation.py
bcbio/pipeline/version.py
bcbio/pipeline/disambiguate/__init__.py
bcbio/pipeline/disambiguate/run.py
bcbio/provenance/__init__.py
bcbio/provenance/data.py
bcbio/provenance/diagnostics.py
bcbio/provenance/do.py
bcbio/provenance/profile.py
bcbio/provenance/programs.py
bcbio/provenance/system.py
bcbio/provenance/versioncheck.py
bcbio/qc/__init__.py
bcbio/qc/coverage.py
bcbio/qc/damage.py
bcbio/qc/fastqc.py
bcbio/qc/kraken.py
bcbio/qc/multiqc.py
bcbio/qc/picard.py
bcbio/qc/qsignature.py
bcbio/qc/qualimap.py
bcbio/qc/samtools.py
bcbio/qc/srna.py
bcbio/qc/umi.py
bcbio/qc/variant.py
bcbio/qc/viral.py
bcbio/rnaseq/__init__.py
bcbio/rnaseq/annotate_gtf.py
bcbio/rnaseq/count.py
bcbio/rnaseq/cpat.py
bcbio/rnaseq/cufflinks.py
bcbio/rnaseq/dexseq.py
bcbio/rnaseq/express.py
bcbio/rnaseq/featureCounts.py
bcbio/rnaseq/gtf.py
bcbio/rnaseq/kallisto.py
bcbio/rnaseq/oncofuse.py
bcbio/rnaseq/qc.py
bcbio/rnaseq/rapmap.py
bcbio/rnaseq/rsem.py
bcbio/rnaseq/sailfish.py
bcbio/rnaseq/salmon.py
bcbio/rnaseq/spikein.py
bcbio/rnaseq/stringtie.py
bcbio/rnaseq/umi.py
bcbio/rnaseq/variation.py
bcbio/server/__init__.py
bcbio/server/background.py
bcbio/server/main.py
bcbio/server/run.py
bcbio/srna/__init__.py
bcbio/srna/group.py
bcbio/srna/mirdeep.py
bcbio/srna/qc.py
bcbio/srna/sample.py
bcbio/structural/__init__.py
bcbio/structural/annotate.py
bcbio/structural/battenberg.py
bcbio/structural/cn_mops.py
bcbio/structural/cnvkit.py
bcbio/structural/convert.py
bcbio/structural/delly.py
bcbio/structural/gridss.py
bcbio/structural/hydra.py
bcbio/structural/lumpy.py
bcbio/structural/manta.py
bcbio/structural/metasv.py
bcbio/structural/pindel.py
bcbio/structural/plot.py
bcbio/structural/prioritize.py
bcbio/structural/regions.py
bcbio/structural/seq2c.py
bcbio/structural/shared.py
bcbio/structural/validate.py
bcbio/structural/wham.py
bcbio/upload/__init__.py
bcbio/upload/filesystem.py
bcbio/upload/galaxy.py
bcbio/upload/irods.py
bcbio/upload/s3.py
bcbio/upload/shared.py
bcbio/variation/__init__.py
bcbio/variation/annotation.py
bcbio/variation/bamprep.py
bcbio/variation/bedutils.py
bcbio/variation/cortex.py
bcbio/variation/coverage.py
bcbio/variation/damage.py
bcbio/variation/effects.py
bcbio/variation/ensemble.py
bcbio/variation/freebayes.py
bcbio/variation/gatk.py
bcbio/variation/gatkfilter.py
bcbio/variation/gatkjoint.py
bcbio/variation/genotype.py
bcbio/variation/germline.py
bcbio/variation/joint.py
bcbio/variation/multi.py
bcbio/variation/multiallelic.py
bcbio/variation/mutect.py
bcbio/variation/mutect2.py
bcbio/variation/naming.py
bcbio/variation/phasing.py
bcbio/variation/platypus.py
bcbio/variation/ploidy.py
bcbio/variation/population.py
bcbio/variation/prioritize.py
bcbio/variation/qsnp.py
bcbio/variation/realign.py
bcbio/variation/recalibrate.py
bcbio/variation/samtools.py
bcbio/variation/scalpel.py
bcbio/variation/sentieon.py
bcbio/variation/split.py
bcbio/variation/validate.py
bcbio/variation/validateplot.py
bcbio/variation/vardict.py
bcbio/variation/varscan.py
bcbio/variation/vcfanno.py
bcbio/variation/vcfutils.py
bcbio/variation/vfilter.py
bcbio/workflow/__init__.py
bcbio/workflow/stormseq.py
bcbio/workflow/template.py
bcbio/workflow/xprize.py
bcbio_nextgen.egg-info/PKG-INFO
bcbio_nextgen.egg-info/SOURCES.txt
bcbio_nextgen.egg-info/dependency_links.txt
bcbio_nextgen.egg-info/not-zip-safe
bcbio_nextgen.egg-info/top_level.txt
config/bcbio_sample.yaml
config/bcbio_system.yaml
config/transfer_info.yaml
scripts/bcbio_fastq_umi_prep.py
scripts/bcbio_nextgen.py
scripts/bcbio_prepare_samples.py
scripts/bcbio_setup_genome.py
scripts/cwltool2wdl.py
tests/__init__.py
tests/conftest.py
tests/data/illumina_samplesheet.csv
tests/data/illumina_samplesheet_fcid_mixed.csv
tests/data/illumina_samplesheet_sampleref_mixed.csv
tests/data/automated/post_process-sample.yaml
tests/data/automated/run_info-bam.yaml
tests/data/automated/run_info-bamclean.yaml
tests/data/automated/run_info-cancer.yaml
tests/data/automated/run_info-cancer2.yaml
tests/data/automated/run_info-chipseq.yaml
tests/data/automated/run_info-cwl.yaml
tests/data/automated/run_info-empty.yaml
tests/data/automated/run_info-explant.yaml
tests/data/automated/run_info-fastrnaseq.yaml
tests/data/automated/run_info-fusion.yaml
tests/data/automated/run_info-fusion_S3.yaml
tests/data/automated/run_info-hisat2.yaml
tests/data/automated/run_info-joint.yaml
tests/data/automated/run_info-rnaseq-variantcall.yaml
tests/data/automated/run_info-rnaseq.yaml
tests/data/automated/run_info-scrnaseq.yaml
tests/data/automated/run_info-srnaseq_bowtie.yaml
tests/data/automated/run_info-srnaseq_star.yaml
tests/data/automated/run_info-star.yaml
tests/data/automated/run_info-stranded.yaml
tests/data/automated/run_info-umi.yaml
tests/data/automated/run_info-variantcall.yaml
tests/data/automated/run_info-variantcall_S3_1.yaml
tests/data/automated/run_info-variantcall_S3_2.yaml
tests/data/automated/run_info.yaml
tests/data/automated/universe_wsgi.ini
tests/data/automated/tool-data/bowtie2_indices.loc
tests/data/automated/tool-data/bowtie_indices.loc
tests/data/automated/tool-data/bwa_index.loc
tests/data/automated/tool-data/mosaik_index.loc
tests/data/automated/tool-data/sam_fa_indices.loc
tests/integration/__init__.py
tests/integration/test_S3_pipelines.py
tests/integration/test_SequencingDump.py
tests/integration/test_automated_analysis.py
tests/integration/test_pipeline.py
tests/unit/__init__.py
tests/unit/data.py
tests/unit/test_alignprep.py