.pylintrc
.resolwebio-filetypes.yml
LICENSE
MANIFEST.in
README.rst
setup.cfg
setup.py
tox.ini
docs/CHANGELOG.rst
docs/catalog-category.rst
docs/catalog-definitions.rst
docs/catalog-types.rst
docs/catalog.rst
docs/conf.py
docs/contributing.rst
docs/descriptor.rst
docs/index.rst
docs/proc.rst
docs/ref.rst
docs/_static/css/custom.css
docs/_templates/page.html
resolwe_bio/__about__.py
resolwe_bio/__init__.py
resolwe_bio/apps.py
resolwe_bio/extensions.py
resolwe_bio/filters.py
resolwe_bio/models.py
resolwe_bio.egg-info/PKG-INFO
resolwe_bio.egg-info/SOURCES.txt
resolwe_bio.egg-info/dependency_links.txt
resolwe_bio.egg-info/not-zip-safe
resolwe_bio.egg-info/requires.txt
resolwe_bio.egg-info/top_level.txt
resolwe_bio/descriptors/amplicon.yml
resolwe_bio/descriptors/bbduk-star-featurecounts.yml
resolwe_bio/descriptors/bbduk-star-htseq.yml
resolwe_bio/descriptors/bcm.yml
resolwe_bio/descriptors/cutadapt-star-htseq.yml
resolwe_bio/descriptors/dicty.yml
resolwe_bio/descriptors/diffexp.yml
resolwe_bio/descriptors/etc.yml
resolwe_bio/descriptors/geneset.yml
resolwe_bio/descriptors/microarray_affy.yml
resolwe_bio/descriptors/reads.yml
resolwe_bio/descriptors/reads_detailed.yml
resolwe_bio/descriptors/rnaseq.yml
resolwe_bio/descriptors/sample_detailed.yml
resolwe_bio/descriptors/sample_geo.yml
resolwe_bio/descriptors/sample_vaccinesurvey.yml
resolwe_bio/descriptors/transmart.yml
resolwe_bio/docker_images/base/Dockerfile.ubuntu-14.04
resolwe_bio/docker_images/base/Dockerfile.ubuntu-16.04
resolwe_bio/docker_images/base/Dockerfile.ubuntu-17.10
resolwe_bio/docker_images/base/Dockerfile.ubuntu-18.04
resolwe_bio/docker_images/base/README.md
resolwe_bio/docker_images/base/common.sh
resolwe_bio/docker_images/chipseq/Dockerfile
resolwe_bio/docker_images/chipseq/README.md
resolwe_bio/docker_images/chipseq/packages-debian-buildreq.txt
resolwe_bio/docker_images/chipseq/packages-debian.txt
resolwe_bio/docker_images/chipseq/packages-manual.txt
resolwe_bio/docker_images/chipseq/packages-python2.txt
resolwe_bio/docker_images/chipseq/packages-r-bioconductor.txt
resolwe_bio/docker_images/chipseq/packages-manual/bamliquidator.sh
resolwe_bio/docker_images/chipseq/packages-manual/wigtobigwig.sh
resolwe_bio/docker_images/dnaseq/Dockerfile
resolwe_bio/docker_images/dnaseq/README.md
resolwe_bio/docker_images/dnaseq/packages-debian-buildreq.txt
resolwe_bio/docker_images/dnaseq/packages-debian.txt
resolwe_bio/docker_images/dnaseq/packages-manual.txt
resolwe_bio/docker_images/dnaseq/packages-python3.txt
resolwe_bio/docker_images/dnaseq/packages-r-bioconductor.txt
resolwe_bio/docker_images/dnaseq/packages-r.txt
resolwe_bio/docker_images/dnaseq/packages-manual/README.txt
resolwe_bio/docker_images/dnaseq/packages-manual/gatk.sh
resolwe_bio/docker_images/dnaseq/packages-manual/lofreq.sh
resolwe_bio/docker_images/dnaseq/packages-manual/primerclip.sh
resolwe_bio/docker_images/dnaseq/packages-manual/r-packages.sh
resolwe_bio/docker_images/dnaseq/packages-manual/samtools.sh
resolwe_bio/docker_images/latex/Dockerfile
resolwe_bio/docker_images/latex/README.md
resolwe_bio/docker_images/latex/packages-debian-buildreq.txt
resolwe_bio/docker_images/latex/packages-debian.txt
resolwe_bio/docker_images/latex/packages-python3.txt
resolwe_bio/docker_images/latex/assets/logo_genialis.pdf
resolwe_bio/docker_images/latex/assets/template_amplicon_report_multi_sample.tex
resolwe_bio/docker_images/latex/packages-manual/.placeholder
resolwe_bio/docker_images/legacy/Dockerfile
resolwe_bio/docker_images/legacy/README.md
resolwe_bio/docker_images/legacy/packages-debian-buildreq.txt
resolwe_bio/docker_images/legacy/packages-debian.txt
resolwe_bio/docker_images/legacy/packages-manual.txt
resolwe_bio/docker_images/legacy/packages-python2-stage2.txt
resolwe_bio/docker_images/legacy/packages-python2.txt
resolwe_bio/docker_images/legacy/packages-python3.txt
resolwe_bio/docker_images/legacy/packages-r-bioconductor.txt
resolwe_bio/docker_images/legacy/packages-r.txt
resolwe_bio/docker_images/legacy/packages-manual/bbmap.sh
resolwe_bio/docker_images/legacy/packages-manual/bcftools.sh
resolwe_bio/docker_images/legacy/packages-manual/bedops.sh
resolwe_bio/docker_images/legacy/packages-manual/bedtools.sh
resolwe_bio/docker_images/legacy/packages-manual/cufflinks.sh
resolwe_bio/docker_images/legacy/packages-manual/ea-utils.sh
resolwe_bio/docker_images/legacy/packages-manual/fastqc.sh
resolwe_bio/docker_images/legacy/packages-manual/genome-tools.sh
resolwe_bio/docker_images/legacy/packages-manual/gotea.sh
resolwe_bio/docker_images/legacy/packages-manual/hisat2.sh
resolwe_bio/docker_images/legacy/packages-manual/hsqutils.sh
resolwe_bio/docker_images/legacy/packages-manual/jbrowse.sh
resolwe_bio/docker_images/legacy/packages-manual/kent-utils.sh
resolwe_bio/docker_images/legacy/packages-manual/lofreq.sh
resolwe_bio/docker_images/legacy/packages-manual/moabs.sh
resolwe_bio/docker_images/legacy/packages-manual/primerclip.sh
resolwe_bio/docker_images/legacy/packages-manual/prinseq.sh
resolwe_bio/docker_images/legacy/packages-manual/r-packages.sh
resolwe_bio/docker_images/legacy/packages-manual/samtools.sh
resolwe_bio/docker_images/legacy/packages-manual/snpeff.sh
resolwe_bio/docker_images/legacy/packages-manual/sra-toolkit.sh
resolwe_bio/docker_images/legacy/packages-manual/star.sh
resolwe_bio/docker_images/legacy/packages-manual/subread.sh
resolwe_bio/docker_images/legacy/packages-manual/trans-decoder.sh
resolwe_bio/docker_images/rnaseq/Dockerfile
resolwe_bio/docker_images/rnaseq/README.md
resolwe_bio/docker_images/rnaseq/packages-debian-buildreq.txt
resolwe_bio/docker_images/rnaseq/packages-debian.txt
resolwe_bio/docker_images/rnaseq/packages-manual.txt
resolwe_bio/docker_images/rnaseq/packages-python3.txt
resolwe_bio/docker_images/rnaseq/packages-r-bioconductor.txt
resolwe_bio/docker_images/rnaseq/packages-r.txt
resolwe_bio/docker_images/rnaseq/packages-manual/bbmap.sh
resolwe_bio/docker_images/rnaseq/packages-manual/cufflinks.sh
resolwe_bio/docker_images/rnaseq/packages-manual/fastqc.sh
resolwe_bio/docker_images/rnaseq/packages-manual/gotea.sh
resolwe_bio/docker_images/rnaseq/packages-manual/hisat2.sh
resolwe_bio/docker_images/rnaseq/packages-manual/r-packages.sh
resolwe_bio/docker_images/rnaseq/packages-manual/rsem.sh
resolwe_bio/docker_images/rnaseq/packages-manual/samtools.sh
resolwe_bio/docker_images/rnaseq/packages-manual/star.sh
resolwe_bio/docker_images/rnaseq/packages-manual/subread.sh
resolwe_bio/docker_images/rnaseq/packages-manual/trimmomatic.sh
resolwe_bio/docker_images/utils/Dockerfile
resolwe_bio/docker_images/utils/README.md
resolwe_bio/docker_images/utils/packages-debian.txt
resolwe_bio/docker_images/utils/packages-manual.txt
resolwe_bio/docker_images/utils/packages-python3.txt
resolwe_bio/docker_images/utils/packages-manual/fastqc.sh
resolwe_bio/docker_images/utils/packages-manual/igvtools.sh
resolwe_bio/docker_images/utils/packages-manual/sra-toolkit.sh
resolwe_bio/expression_filters/__init__.py
resolwe_bio/expression_filters/sample.py
resolwe_bio/fixtures/relationtypes.yaml
resolwe_bio/kb/__init__.py
resolwe_bio/kb/admin.py
resolwe_bio/kb/apps.py
resolwe_bio/kb/elastic_indexes.py
resolwe_bio/kb/filters.py
resolwe_bio/kb/models.py
resolwe_bio/kb/serializers.py
resolwe_bio/kb/views.py
resolwe_bio/kb/management/__init__.py
resolwe_bio/kb/management/commands/__init__.py
resolwe_bio/kb/management/commands/insert_features.py
resolwe_bio/kb/management/commands/insert_mappings.py
resolwe_bio/kb/management/commands/utils.py
resolwe_bio/kb/migrations/0001_initial.py
resolwe_bio/kb/migrations/0002_alter_field_max_length.py
resolwe_bio/kb/migrations/0003_add_map_index.py
resolwe_bio/kb/migrations/0004_add_unique_together.py
resolwe_bio/kb/migrations/0005_species.py
resolwe_bio/kb/migrations/__init__.py
resolwe_bio/kb/tests/__init__.py
resolwe_bio/kb/tests/test_feature.py
resolwe_bio/kb/tests/test_import_kb.py
resolwe_bio/kb/tests/test_mapping.py
resolwe_bio/management/__init__.py
resolwe_bio/management/commands/__init__.py
resolwe_bio/management/commands/generate_diffexpr_cuffdiff.py
resolwe_bio/management/commands/generate_diffexpr_deseq.py
resolwe_bio/management/commands/generate_etc.py
resolwe_bio/management/commands/generate_geneset.py
resolwe_bio/management/commands/generate_samples.py
resolwe_bio/management/commands/utils.py
resolwe_bio/migrations/0001_initial.py
resolwe_bio/migrations/0002_sample_presample.py
resolwe_bio/migrations/0003_fix_jsonfields.py
resolwe_bio/migrations/0004_add_owner.py
resolwe_bio/migrations/0005_make_date_indexes.py
resolwe_bio/migrations/0006_alter_versionfield.py
resolwe_bio/migrations/0007_sample_descriptor_dirty.py
resolwe_bio/migrations/0008_migrate_sample.py
resolwe_bio/migrations/0009_delete_sample.py
resolwe_bio/migrations/0010_add_relation_types.py
resolwe_bio/migrations/__init__.py
resolwe_bio/processes/WGBS/bsmap.yml
resolwe_bio/processes/WGBS/mcall.yml
resolwe_bio/processes/alignment/abstract.yml
resolwe_bio/processes/alignment/bowtie.yml
resolwe_bio/processes/alignment/bwa.yml
resolwe_bio/processes/alignment/hisat2.yml
resolwe_bio/processes/alignment/star.yml
resolwe_bio/processes/alignment/subread.yml
resolwe_bio/processes/alignment/tophat.yml
resolwe_bio/processes/amplicon/amplicon_table.yml
resolwe_bio/processes/amplicon/bwa_trim.yml
resolwe_bio/processes/amplicon/target_metrics.yml
resolwe_bio/processes/annotation/abstract.yml
resolwe_bio/processes/annotation/cuffmerge.yml
resolwe_bio/processes/annotation/feature_location.yml
resolwe_bio/processes/assembly/abyss.yml
resolwe_bio/processes/chip_seq/macs14.yml
resolwe_bio/processes/chip_seq/macs2.yml
resolwe_bio/processes/chip_seq/rose2.yml
resolwe_bio/processes/chip_seq/scoring.yml
resolwe_bio/processes/clustering/find_similar.yml
resolwe_bio/processes/clustering/hierarchical_clustering.yml
resolwe_bio/processes/clustering/pca.yml
resolwe_bio/processes/differential_expression/abstract.yml
resolwe_bio/processes/differential_expression/cuffdiff.yml
resolwe_bio/processes/differential_expression/deseq.yml
resolwe_bio/processes/differential_expression/edgeR.yml
resolwe_bio/processes/differential_expression/limma.yml
resolwe_bio/processes/exome_coverage/coverage_report.yml
resolwe_bio/processes/exome_coverage/coveragebed.yml
resolwe_bio/processes/expression/abstract.yml
resolwe_bio/processes/expression/cufflinks.yml
resolwe_bio/processes/expression/cuffnorm.yml
resolwe_bio/processes/expression/cuffquant.yml
resolwe_bio/processes/expression/dicty_bcm.yml
resolwe_bio/processes/expression/etc.yml
resolwe_bio/processes/expression/expression_aggregator.yml
resolwe_bio/processes/expression/featureCounts.yml
resolwe_bio/processes/expression/htseq_count.yml
resolwe_bio/processes/expression/index_fasta_nucl.yml
resolwe_bio/processes/expression/mappability.yml
resolwe_bio/processes/expression/merge_etc.yml
resolwe_bio/processes/expression/merge_expressions.yml
resolwe_bio/processes/expression/rsem.yml
resolwe_bio/processes/expression/salmon_index.yml
resolwe_bio/processes/genome_browser/igv_bam.yml
resolwe_bio/processes/go_enrichment/go.yml
resolwe_bio/processes/import_data/abstract_bed.yml
resolwe_bio/processes/import_data/annotation.yml
resolwe_bio/processes/import_data/annotation_bed.yml
resolwe_bio/processes/import_data/bam.yml
resolwe_bio/processes/import_data/basespace.yml
resolwe_bio/processes/import_data/cuffquant.yml
resolwe_bio/processes/import_data/differential_exp.yml
resolwe_bio/processes/import_data/etc.yml
resolwe_bio/processes/import_data/expressions.yml
resolwe_bio/processes/import_data/geneset.yml
resolwe_bio/processes/import_data/genome.yml
resolwe_bio/processes/import_data/go_gaf.yml
resolwe_bio/processes/import_data/go_obo.yml
resolwe_bio/processes/import_data/hmmer_database.yml
resolwe_bio/processes/import_data/mappability_bigwig.yml
resolwe_bio/processes/import_data/mappability_tab.yml
resolwe_bio/processes/import_data/master_file.yml
resolwe_bio/processes/import_data/microarray_affy.yml
resolwe_bio/processes/import_data/nucleotide_seq.yml
resolwe_bio/processes/import_data/pathway_map.yml
resolwe_bio/processes/import_data/sam_header.yml
resolwe_bio/processes/import_data/seq_reads.yml
resolwe_bio/processes/import_data/seq_reads_multiplexed.yml
resolwe_bio/processes/import_data/snpeff.yml
resolwe_bio/processes/import_data/sra_file.yml
resolwe_bio/processes/import_data/target_pcr_metrics.yml
resolwe_bio/processes/import_data/variants_bed.yml
resolwe_bio/processes/import_data/variants_vcf.yml
resolwe_bio/processes/jbrowse/annotation_bed.yml
resolwe_bio/processes/jbrowse/annotation_gff3.yml
resolwe_bio/processes/jbrowse/annotation_gtf.yml
resolwe_bio/processes/jbrowse/bam_coverage.yml
resolwe_bio/processes/jbrowse/bam_coverage_normalized.yml
resolwe_bio/processes/jbrowse/refseq.yml
resolwe_bio/processes/microarray/microarray_qc.yml
resolwe_bio/processes/plots/bamliquidator.yml
resolwe_bio/processes/plots/bamplot.yml
resolwe_bio/processes/reads_processing/bbduk.yml
resolwe_bio/processes/reads_processing/cutadapt.yml
resolwe_bio/processes/reads_processing/cutadapt_amplicon.yml
resolwe_bio/processes/reads_processing/cutadapt_custom.yml
resolwe_bio/processes/reads_processing/fastq_mcf.yml
resolwe_bio/processes/reads_processing/hsqutils.yml
resolwe_bio/processes/reads_processing/merge_to_paired_end.yml
resolwe_bio/processes/reads_processing/prinseq_lite.yml
resolwe_bio/processes/reads_processing/sortmerna.yml
resolwe_bio/processes/reads_processing/trimmomatic.yml
resolwe_bio/processes/reports/amplicon_multi_report.yml
resolwe_bio/processes/reports/amplicon_report.yml
resolwe_bio/processes/support_processors/archive.yml
resolwe_bio/processes/support_processors/bam_coverage.yml
resolwe_bio/processes/support_processors/bam_split.yml
resolwe_bio/processes/support_processors/gff_to_gtf.yml
resolwe_bio/processes/support_processors/library_strandedness.yml
resolwe_bio/processes/support_processors/prepare_geo.yml
resolwe_bio/processes/support_processors/refseq_compatibility.yml
resolwe_bio/processes/transmart/import.yml
resolwe_bio/processes/unit_tests/test_basic_fields.yml
resolwe_bio/processes/unit_tests/test_disabled_fields.yml
resolwe_bio/processes/unit_tests/test_hidden_fields.yml
resolwe_bio/processes/unit_tests/test_list.yml
resolwe_bio/processes/unit_tests/test_sleep_progress.yml
resolwe_bio/processes/variant_calling/filtering_chemut.yml
resolwe_bio/processes/variant_calling/gatk.yml
resolwe_bio/processes/variant_calling/hsqutils-dedup.yml
resolwe_bio/processes/variant_calling/lofreq.yml
resolwe_bio/processes/variant_calling/preprocess_bam.yml
resolwe_bio/processes/variant_calling/samtools.yml
resolwe_bio/processes/variant_calling/snpeff.yml
resolwe_bio/processes/variant_calling/vc_chemut.yml
resolwe_bio/processes/workflows/amplicon.yml
resolwe_bio/processes/workflows/bbduk_star_featurecounts.yml
resolwe_bio/processes/workflows/bbduk_star_htseq.yml
resolwe_bio/processes/workflows/chemut.yml
resolwe_bio/processes/workflows/chip_seq.yml
resolwe_bio/processes/workflows/cuffquant.yml
resolwe_bio/processes/workflows/cutadapt_star_htseq.yml
resolwe_bio/processes/workflows/cutadapt_star_rsem.yml
resolwe_bio/processes/workflows/heat_seq.yml
resolwe_bio/processes/workflows/mirna.yml
resolwe_bio/processes/workflows/rnaseq.yml
resolwe_bio/processes/workflows/wgbs.yml
resolwe_bio/tests/__init__.py
resolwe_bio/tests/commands/__init__.py
resolwe_bio/tests/commands/test_generators.py
resolwe_bio/tests/files/.DS_Store
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resolwe_bio/tools/fastqc.sh
resolwe_bio/tools/feature_location.py
resolwe_bio/tools/find_similar.py
resolwe_bio/tools/format_index_files.py
resolwe_bio/tools/garvan_coverage.py
resolwe_bio/tools/genehcluster.py
resolwe_bio/tools/geneset2storage.py
resolwe_bio/tools/gff3_to_gtf.py
resolwe_bio/tools/go_genesets.py
resolwe_bio/tools/goea.py
resolwe_bio/tools/importETC.py
resolwe_bio/tools/lofreq2_indel_ovlp.py
resolwe_bio/tools/make_amplicon_table.py
resolwe_bio/tools/make_igv_session.py
resolwe_bio/tools/make_igv_session_archive.py
resolwe_bio/tools/make_multireport.py
resolwe_bio/tools/make_report.py
resolwe_bio/tools/mappability.py
resolwe_bio/tools/mergebowtie2stats.py
resolwe_bio/tools/mergebowtie2stats_paired.py
resolwe_bio/tools/mergebowtiestats.py
resolwe_bio/tools/mergeetc.py
resolwe_bio/tools/microarrayQC.R
resolwe_bio/tools/parse_closest_features.R
resolwe_bio/tools/parse_cuffnorm.py
resolwe_bio/tools/parse_diffexp.py
resolwe_bio/tools/parse_encoding_type.py
resolwe_bio/tools/parse_library_type.py
resolwe_bio/tools/parse_star_expressions.py
resolwe_bio/tools/pca.py
resolwe_bio/tools/peak2geneScore.R
resolwe_bio/tools/plot_enhancers.py
resolwe_bio/tools/plotcoverage_html.py
resolwe_bio/tools/rnaseq.py
resolwe_bio/tools/run_edger.R
resolwe_bio/tools/run_limma.R
resolwe_bio/tools/samplehcluster.py
resolwe_bio/tools/transmart_fetch.R
resolwe_bio/tools/transmart_import.py
resolwe_bio/tools/transmart_utils.py
resolwe_bio/tools/unique_sample_names.py
resolwe_bio/tools/utils.py
resolwe_bio/tools/validate_master_file.py
resolwe_bio/tools/volcanoplot.py
resolwe_bio/tools/xexpression.py
resolwe_bio/tools/xgff.py
resolwe_bio/tools/xgtf2gff.py
resolwe_bio/tools/xtabcoverage.py
resolwe_bio/utils/__init__.py
resolwe_bio/utils/filter.py
resolwe_bio/utils/test.py
tests/.env
tests/__init__.py
tests/docker-compose.yml
tests/manage.py
tests/routing.py
tests/settings.py
tests/urls.py
tests/fixtures/collection.yaml
tests/fixtures/data.yaml
tests/test_data/README.rst
tests/test_runtime/README.rst
tests/test_upload/README.rst