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Release 1.12.0
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iainrb committed Apr 8, 2016
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25 changes: 25 additions & 0 deletions doc/CHANGELOG.md
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Expand Up @@ -11,6 +11,27 @@ Added:
- Replace old identity check with new Bayesian version in "main" QC output
and plots


Release 1.12.0: 2016-04-07
--------------------------

Added:
- New ready_workflow.pl script to query iRODS for QC plex data, write VCF,
generate config YML, and set up an analysis directory
- Ruby workflows can read multiple VCF and plex manifest paths from
YML, and input them to the quality_control pipeline task
- Revised default pass threshold for Bayesian identity check

Removed:
- genotyping_yml.pl and tests; functionality replaced by ready_workflow.pl
- Annotation modules exporting constants for irods metadata; constants have
been relocated to Metadata.pm in wtsi-npg/perl-irods-wrap

Fixed:
- Refactored run_qc.pl for better handling of command-line arguments
- Updated for compatibility with latest dependency versions


Release 1.11.6: 2016-02-08
--------------------------

Expand All @@ -19,6 +40,7 @@ Fixed:
the SequenceScape warehouse that was not specific enough to allow it
to proceed when a sample had been analysed more than once.


Release 1.11.5: 2015-12-15
--------------------------

Expand All @@ -34,13 +56,15 @@ Added:
- Find genome reference path from iRODS metadata for VCF header; adds
dependency on wtsi-npg/npg_tracking


Release 1.11.4: 2015-10-09
--------------------------

Fixed:
- Bug in publish_infinium_genotypes.pl which caused it to exit when it
detected bad or missing data. It now detects these files and skips them.


Release 1.11.3: 2015-09-18
--------------------------

Expand All @@ -53,6 +77,7 @@ Fixed:
Changed:
- bcftools version upgraded to 1.2


Release 1.11.2: 2015-08-24
--------------------------

Expand Down
33 changes: 18 additions & 15 deletions src/perl/Build.PL
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Original file line number Diff line number Diff line change
Expand Up @@ -29,21 +29,22 @@ my $build = Build->new
'Test::Compile' => 0
},
requires => {
'Config::IniFiles' => '>= 2.8.6',
'DBI' => '>= 1.63',
'DBIx::Class' => '>= 0.082',
'Data::Dump' => '>= 1.22',
'DateTime' => '>= 1.18',
'List::AllUtils' => '>= 0.09',
'Log::Log4perl' => '>= 1.46',
'Moose' => '>= 2.1',
'MooseX::Types' => '>= 0.45',
'Set::Scalar' => '>= 1.29',
'Text::CSV' => '>= 1.33',
'Try::Tiny' => '>= 0.22',
'URI' => '>= 1.67',
'WTSI::DNAP::Warehouse::Schema' => '>= 1.1',
'WTSI::NPG::iRODS' => '>= 0.15.0'
'Config::IniFiles' => '>= 2.8.6',
'DBI' => '>= 1.63',
'DBIx::Class' => '>= 0.082',
'Data::Dump' => '>= 1.22',
'DateTime' => '>= 1.18',
'List::AllUtils' => '>= 0.09',
'Log::Log4perl' => '>= 1.46',
'Moose' => '>= 2.1',
'MooseX::Types' => '>= 0.45',
'npg_tracking::data::reference::find' => '>= 84.8',
'Set::Scalar' => '>= 1.29',
'Text::CSV' => '>= 1.33',
'Try::Tiny' => '>= 0.22',
'URI' => '>= 1.67',
'WTSI::DNAP::Warehouse::Schema' => '>= 1.1',
'WTSI::NPG::iRODS' => '>= 0.15.0'
},
recommends => {
'UUID' => '>= 0.24',
Expand All @@ -56,6 +57,8 @@ my $build = Build->new
'etc/states.ini' => 'etc/states.ini' },
conf_files => {'etc/log4perl.conf' => 'etc/log4perl.conf',
'etc/qc_config.json' => 'etc/qc_config.json',
'etc/ready_qc_fluidigm.json' => 'etc/ready_qc_fluidigm.json',
'etc/ready_qc_sequenom.json' => 'etc/ready_qc_sequenom.json',
'etc/illuminus_prefilter.json' => 'etc/illuminus_prefilter.json',
'etc/zcall_prefilter.json' => 'etc/zcall_prefilter.json',
'etc/reportIntro.tex' => 'etc/reportIntro.tex',
Expand Down
36 changes: 23 additions & 13 deletions src/perl/MANIFEST
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ bin/create_test_database.pl
bin/filter_illuminus_output.pl
bin/find_modified_files.pl
bin/gendermix_standalone.pl
bin/genotyping_yml.pl
bin/identity_simulation.pl
bin/illuminus.pl
bin/manifest_plex_intersection.pl
bin/plate_heatmap_index.pl
Expand Down Expand Up @@ -72,7 +72,6 @@ lib/WTSI/NPG/Database/DBIx.pm
lib/WTSI/NPG/Database/MLWarehouse.pm
lib/WTSI/NPG/Database/Warehouse.pm
lib/WTSI/NPG/Expression/AnalysisPublisher.pm
lib/WTSI/NPG/Expression/Annotation.pm
lib/WTSI/NPG/Expression/Annotator.pm
lib/WTSI/NPG/Expression/ChipLoadingManifest.pm
lib/WTSI/NPG/Expression/ChipLoadingManifestV1.pm
Expand All @@ -83,7 +82,6 @@ lib/WTSI/NPG/Expression/Publisher.pm
lib/WTSI/NPG/Expression/ResultSet.pm
lib/WTSI/NPG/Expression/SampleProbeProfile.pm
lib/WTSI/NPG/Genotyping.pm
lib/WTSI/NPG/Genotyping/Annotation.pm
lib/WTSI/NPG/Genotyping/Annotator.pm
lib/WTSI/NPG/Genotyping/Call.pm
lib/WTSI/NPG/Genotyping/Database/Infinium.pm
Expand Down Expand Up @@ -137,6 +135,7 @@ lib/WTSI/NPG/Genotyping/QC/QCPlotTests.pm
lib/WTSI/NPG/Genotyping/QC/Reports.pm
lib/WTSI/NPG/Genotyping/QC/SnpID.pm
lib/WTSI/NPG/Genotyping/QC_wip/Check/Identity.pm
lib/WTSI/NPG/Genotyping/QC_wip/Check/IdentitySimulator.pm
lib/WTSI/NPG/Genotyping/QC_wip/Check/SampleIdentityBayesian.pm
lib/WTSI/NPG/Genotyping/Reference.pm
lib/WTSI/NPG/Genotyping/Sequenom/AssayDataObject.pm
Expand All @@ -156,6 +155,7 @@ lib/WTSI/NPG/Genotyping/VCF/GtcheckWrapper.pm
lib/WTSI/NPG/Genotyping/VCF/Header.pm
lib/WTSI/NPG/Genotyping/VCF/HeaderParser.pm
lib/WTSI/NPG/Genotyping/VCF/Parser.pm
lib/WTSI/NPG/Genotyping/VCF/PlexResultFinder.pm
lib/WTSI/NPG/Genotyping/VCF/ReferenceFinder.pm
lib/WTSI/NPG/Genotyping/VCF/Slurper.pm
lib/WTSI/NPG/Genotyping/VCF/VCFDataSet.pm
Expand Down Expand Up @@ -349,6 +349,7 @@ t/fluidigm_resultset/missing_tif/0123456789/0123456789.csv
t/fluidigm_resultset/missing_tif/0123456789/Data/athos.tif
t/fluidigm_resultset/missing_tif/0123456789/Data/porthos.tif
t/fluidigm_subscriber.t
t/fluidigm_subscriber/chromosome_lengths_GRCh37.json
t/fluidigm_subscriber/qc.tsv
t/fluidigm_subscriber/S01_1381735059.csv
t/fluidigm_subscriber/S01_1381735060.csv
Expand All @@ -366,14 +367,10 @@ t/gender/input_xhet_large.txt
t/gender_marker.t
t/gender_marker_call.t
t/gender_standalone.t
t/genotyping_yml.t
t/genotyping_yml/config.yml
t/genotyping_yml/genotype_illuminus.yml
t/genotyping_yml/genotype_zcall.yml
t/genotyping_yml/genotyping_DUMMY.db
t/identity.t
t/identity_check_sample_wip_bayesian.t
t/identity_check_wip.t
t/identity_simulation_wip.t
t/illuminus.t
t/illuminus/example.json
t/illuminus/example_all.iln
Expand Down Expand Up @@ -441,6 +438,9 @@ t/publisher.t
t/publisher/lorem.txt
t/publisher/update/lorem.txt
t/qc/.gitattributes
t/qc/check/identity/combined_identity_expected.json
t/qc/check/identity/expected_identity_results.json
t/qc/check/identity/expected_omit_results.json
t/qc/check/identity/fake_genotyping.db
t/qc/check/identity/fake_qc_genotypes.bed
t/qc/check/identity/fake_qc_genotypes.bim
Expand All @@ -452,9 +452,17 @@ t/qc/check/identity/fake_swap_genotypes.bim
t/qc/check/identity/fake_swap_genotypes.fam
t/qc/check/identity/fake_swap_genotypes.map
t/qc/check/identity/fake_swap_genotypes.ped
t/qc/check/identity/identity_script_output.csv
t/qc/check/identity/identity_script_output.json
t/qc/check/identity/identity_script_output_alternate_prior.json
t/qc/check/identity/qc_plex_calls.vcf
t/qc/check/identity/qc_plex_calls_1.vcf
t/qc/check/identity/qc_plex_calls_2.vcf
t/qc/check/identity/simulated_ecp.txt
t/qc/check/identity/simulated_qcr.txt
t/qc/check/identity/simulated_qcs.txt
t/qc/check/identity/simulated_smp.txt
t/qc/check/identity/simulated_xer.txt
t/qc/check/identity/W30467_snp_set_info_1000Genomes.tsv
t/qc/check/identity/W30467_snp_set_info_1000Genomes_1.tsv
t/qc/check/identity/W30467_snp_set_info_1000Genomes_2.tsv
Expand All @@ -467,6 +475,7 @@ t/qc_test_data/output_examples/identity_check.json
t/qc_test_data/output_examples/magnitude.txt
t/qc_test_data/output_examples/qc_exclusions.json
t/qc_test_data/output_examples/qc_metrics.json
t/qc_test_data/output_examples/qc_results.csv
t/qc_test_data/output_examples/qc_results.json
t/qc_test_data/output_examples/sample_cr_het.txt
t/qc_test_data/output_examples/sample_xhet_gender.txt
Expand All @@ -491,7 +500,7 @@ t/query_project_samples.t
t/query_project_samples/sample1.gtc
t/query_project_samples/sample1_Grn.idat
t/query_project_samples/sample1_Red.idat
t/ready_plex.t
t/ready_workflow.t
t/reference_finder.t
t/reports.t
t/reports/crHetDensityHeatmap.pdf
Expand Down Expand Up @@ -606,6 +615,7 @@ t/sequenom_assay_result.t
t/sequenom_assay_resultset.t
t/sequenom_publisher.t
t/sequenom_subscriber.t
t/sequenom_subscriber/chromosome_lengths_GRCh37.json
t/sequenom_subscriber/sequenom_001.csv
t/sequenom_subscriber/sequenom_002.csv
t/sequenom_subscriber/sequenom_003.csv
Expand Down Expand Up @@ -653,7 +663,6 @@ t/vcf/fluidigm_004.csv
t/vcf/fluidigm_header_1.txt
t/vcf/fluidigm_header_2.txt
t/vcf/fluidigm_inputs.txt
t/vcf/fluidigm_samples.json
t/vcf/pairwise_discordance_fluidigm.json
t/vcf/pairwise_discordance_sequenom.json
t/vcf/qc_fluidigm_snp_info_GRCh37.tsv
Expand All @@ -667,7 +676,6 @@ t/vcf/sequenom_alternate_snp_002.csv
t/vcf/sequenom_alternate_snp_003.csv
t/vcf/sequenom_alternate_snp_004.csv
t/vcf/sequenom_inputs.txt
t/vcf/sequenom_samples.json
t/vcf/W30467_snp_set_info_GRCh37.tsv
t/vcf/W30467_snp_set_info_GRCh37_1.tsv
t/WTSI/NPG/Database/MLWarehouseTest.pm
Expand Down Expand Up @@ -700,7 +708,9 @@ t/WTSI/NPG/Genotyping/Infinium/InfiniumDataObjectTest.pm
t/WTSI/NPG/Genotyping/Infinium/PublisherTest.pm
t/WTSI/NPG/Genotyping/Infinium/ResultSetTest.pm
t/WTSI/NPG/Genotyping/Infinium/SampleQueryTest.pm
t/WTSI/NPG/Genotyping/QC/CollationTest.pm
t/WTSI/NPG/Genotyping/QC/IdentityTest.pm
t/WTSI/NPG/Genotyping/QC_wip/Check/IdentitySimulatorTest.pm
t/WTSI/NPG/Genotyping/QC_wip/Check/IdentityTest.pm
t/WTSI/NPG/Genotyping/QC_wip/Check/SampleIdentityBayesianTest.pm
t/WTSI/NPG/Genotyping/ScriptsTest.pm
Expand All @@ -713,11 +723,11 @@ t/WTSI/NPG/Genotyping/SNPSetPublisherTest.pm
t/WTSI/NPG/Genotyping/SNPSetTest.pm
t/WTSI/NPG/Genotyping/SNPTest.pm
t/WTSI/NPG/Genotyping/UpdatePlinkAnnotationTest.pm
t/WTSI/NPG/Genotyping/VCF/ReadyPlexCallsTest.pm
t/WTSI/NPG/Genotyping/VCF/ReadyWorkflowTest.pm
t/WTSI/NPG/Genotyping/VCF/ReferenceFinderTest.pm
t/WTSI/NPG/Genotyping/VCF/VCFTest.pm
t/WTSI/NPG/Genotyping/YMLTest.pm
t/WTSI/NPG/PublisherTest.pm
t/WTSI/NPG/SimplePublisherTest.pm
t/WTSI/NPG/Test.pm
t/WTSI/NPG/UtilitiesTest.pm
t/wtsi_genotyping.t
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