LICENSE
MANIFEST.in
README.md
requirements-dev.txt
requirements.txt
setup.cfg
setup.py
housekeeper/__init__.py
housekeeper/constants.py
housekeeper/exc.py
housekeeper/initiate.py
housekeeper.egg-info/PKG-INFO
housekeeper.egg-info/SOURCES.txt
housekeeper.egg-info/dependency_links.txt
housekeeper.egg-info/entry_points.txt
housekeeper.egg-info/not-zip-safe
housekeeper.egg-info/requires.txt
housekeeper.egg-info/top_level.txt
housekeeper/archive/__init__.py
housekeeper/archive/cli.py
housekeeper/archive/core.py
housekeeper/cli/__init__.py
housekeeper/cli/base.py
housekeeper/cli/core.py
housekeeper/cli/log.py
housekeeper/cli/utils.py
housekeeper/compile/__init__.py
housekeeper/compile/cli.py
housekeeper/compile/core.py
housekeeper/compile/restore.py
housekeeper/compile/tar.py
housekeeper/deliver/__init__.py
housekeeper/deliver/rsync.py
housekeeper/pipelines/__init__.py
housekeeper/pipelines/cli.py
housekeeper/pipelines/general/__init__.py
housekeeper/pipelines/general/add.py
housekeeper/pipelines/general/commit.py
housekeeper/pipelines/mip/__init__.py
housekeeper/pipelines/mip/build.py
housekeeper/pipelines/mip/core.py
housekeeper/pipelines/mip/meta.py
housekeeper/pipelines/mip/parse.py
housekeeper/pipelines/mip/prepare.py
housekeeper/pipelines/mip2/__init__.py
housekeeper/pipelines/mip2/core.py
housekeeper/pipelines/mip2/prepare.py
housekeeper/pipelines/miparchive/__init__.py
housekeeper/pipelines/miparchive/core.py
housekeeper/pipelines/miparchive/prepare.py
housekeeper/server/__init__.py
housekeeper/server/app.py
housekeeper/store/__init__.py
housekeeper/store/api.py
housekeeper/store/cli.py
housekeeper/store/models.py
housekeeper/store/utils.py
tests/conftest.py
tests/test_cli.py
tests/test_initiate.py
tests/archive/test_archive_core.py
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/16074.fam
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/16074_qcmetrics.yaml
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/qc_pedigree.yaml
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/bwa/gatk/16074_sorted_md_rreal_brecal_comb_SV.bcf
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/bwa/gatk/16074_sorted_md_rreal_brecal_comb_vep_parsed_ranked_SV.bcf
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/bwa/gatk/16074_sorted_md_rreal_brecal_comb_vep_parsed_ranked_SV.selected.bcf
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/bwa/gatk/16074_sorted_md_rreal_brecal_comb_vep_parsed_ranked_SV.selected.vcf
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/bwa/gatk/16074_sorted_md_rreal_brecal_comb_vep_parsed_ranked_SV.vcf
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/bwa/gatk/16074_sorted_md_rreal_brecal_gvcf_vrecal_comb_BOTH.bcf
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/bwa/gatk/16074_sorted_md_rreal_brecal_gvcf_vrecal_comb_BOTH.bcf.csi
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/bwa/gatk/16074_sorted_md_rreal_brecal_gvcf_vrecal_comb_vt_vep_parsed_snpeff_ranked_BOTH.bcf
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/bwa/gatk/16074_sorted_md_rreal_brecal_gvcf_vrecal_comb_vt_vep_parsed_snpeff_ranked_BOTH.selected.bcf
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/bwa/gatk/16074_sorted_md_rreal_brecal_gvcf_vrecal_comb_vt_vep_parsed_snpeff_ranked_BOTH.selected.vcf
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/bwa/gatk/16074_sorted_md_rreal_brecal_gvcf_vrecal_comb_vt_vep_parsed_snpeff_ranked_BOTH.vcf
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/mip_log/2016-06-27/mip.pl_2016-06-27T15:06:51.log
tests/fixtures/mip/cust003/16074/analysis/genomes/16074/mip_log/2016-06-27/mip.pl_2016-06-27T15:06:51.log.status
tests/fixtures/mip/cust003/16074/analysis/genomes/ADM1594A12/bwa/ADM1594A12.160623_HNCLTCCXX-11-Undetermined_CTGAAGCT.lane7_sorted.cram
tests/fixtures/mip/cust003/16074/analysis/genomes/ADM1594A12/bwa/ADM1594A12.160623_HNCLTCCXX-11_CTGAAGCT.lane7_sorted.cram
tests/fixtures/mip/cust003/16074/analysis/genomes/ADM1594A12/bwa/ADM1594A12.160623_HNCLTCCXX-21-Undetermined_CTGAAGCT.lane7_sorted.cram
tests/fixtures/mip/cust003/16074/analysis/genomes/ADM1594A12/bwa/ADM1594A12.160623_HNCLTCCXX-21_CTGAAGCT.lane7_sorted.cram
tests/fixtures/mip/cust003/16074/analysis/genomes/ADM1594A12/bwa/ADM1594A12_lanes_7777_sorted_md_metric
tests/fixtures/mip/cust003/16074/analysis/genomes/ADM1594A12/bwa/coveragereport/ADM1594A12_lanes_7777_sorted_md_rreal_brecal_coverage.bed
tests/fixtures/mip/cust003/16074/analysis/genomes/ADM1594A12/bwa/gatk/ADM1594A12_lanes_7777_sorted_md_rreal_brecal.bam
tests/fixtures/mip/cust003/16074/analysis/genomes/ADM1594A12/bwa/gatk/ADM1594A12_lanes_7777_sorted_md_rreal_brecal.bam.bai
tests/fixtures/mip/cust003/16074/analysis/genomes/ADM1594A12/multiqc/multiqc_data/multiqc_samtools.txt
tests/fixtures/mip/cust003/16074/genomes/16074/16074_config.yaml
tests/fixtures/mip/cust003/16074/genomes/16074/16074_pedigree.txt
tests/fixtures/mip/cust003/16074/genomes/16074/16074_qc_sampleInfo.yaml
tests/fixtures/mip2/cust003/15068/analysis/exomes/meta.yaml
tests/fixtures/mip2/cust003/15068/analysis/exomes/15068/qc_pedigree.yaml
tests/fixtures/mip2/cust003/15068/analysis/exomes/15068/bwa/gatk/15068_sorted_pmd_rreal_brecal_gvcf_vrecal_vep_parsed_snpeff_ranked_BOTH.selected.vcf
tests/fixtures/mip2/cust003/15068/analysis/exomes/15068/bwa/gatk/15068_sorted_pmd_rreal_brecal_gvcf_vrecal_vep_parsed_snpeff_ranked_BOTH.vcf
tests/fixtures/mip2/cust003/15068/exomes/15068/15068_config.yaml
tests/fixtures/mip2/cust003/15068/exomes/15068/15068_pedigree.txt
tests/fixtures/mip2/cust003/15068/exomes/15068/15068_qc_sampleInfo.yaml
tests/fixtures/miparchive/015701600403fam/exomes/015701600403fam/015701600403fam_config.yaml
tests/fixtures/miparchive/015701600403fam/exomes/015701600403fam/015701600403fam_pedigree.txt
tests/fixtures/miparchive/015701600403fam/exomes/015701600403fam/015701600403fam_qc_sampleInfo.yaml
tests/fixtures/miparchive/015701600403fam/exomes/015701600403fam/archive/meta.yaml
tests/fixtures/miparchive/015701600403fam/exomes/015701600403fam/archive/015701600403fam/015701600403fam_qcmetrics.yaml
tests/fixtures/miparchive/015701600403fam/exomes/015701600403fam/archive/015701600403fam/015701600403fam_sorted_pmd_rreal_brecal_gvcf_vrecal_BOTH.bcf
tests/fixtures/miparchive/015701600403fam/exomes/015701600403fam/archive/015701600403fam/015701600403fam_sorted_pmd_rreal_brecal_gvcf_vrecal_BOTH.bcf.csi
tests/fixtures/miparchive/015701600403fam/exomes/015701600403fam/archive/015701600403fam/015701600403fam_sorted_pmd_rreal_brecal_gvcf_vrecal_vt_vep_parsed_snpeff_ranked_BOTH.selected.vcf
tests/fixtures/miparchive/015701600403fam/exomes/015701600403fam/archive/015701600403fam/015701600403fam_sorted_pmd_rreal_brecal_gvcf_vrecal_vt_vep_parsed_snpeff_ranked_BOTH.vcf
tests/fixtures/miparchive/015701600403fam/exomes/015701600403fam/archive/015701600403fam/mip.pl_2015-11-30T14:06:55.log
tests/fixtures/miparchive/015701600403fam/exomes/015701600403fam/archive/015701600403fam/qc_pedigree.yaml
tests/fixtures/miparchive/015701600403fam/exomes/015701600403fam/archive/ADM1221A1/ADM1221A1.151127_HF5F2BCXX_ACAAGCTA.lane1_sorted.cram
tests/fixtures/miparchive/015701600403fam/exomes/015701600403fam/archive/ADM1221A1/ADM1221A1.151127_HF5F2BCXX_ACAAGCTA.lane2_sorted.cram
tests/pipelines/test_pipelines_cli.py
tests/pipelines/general/test_pipelines_general_add.py
tests/pipelines/mip/test_pipelines_mip_prepare.py
tests/store/test_store_models.py
tests/store/test_store_utils.py