| 679e196 | Thomas Mooney | 06 July 2015, 20:55:27 UTC | Don't worry about design set reference. | 06 July 2015, 20:55:27 UTC |
| 3fb81bf | Eddie Belter | 06 July 2015, 20:41:01 UTC | RefCov Metrics: use subtests and plan | 06 July 2015, 20:41:01 UTC |
| 8e90b3d | Eddie Belter | 06 July 2015, 20:36:43 UTC | RefCov Metrics: add alignment test | 06 July 2015, 20:36:43 UTC |
| 6be2c6a | Eddie Belter | 06 July 2015, 20:19:01 UTC | RefCov Metrics: chmod 664 | 06 July 2015, 20:19:01 UTC |
| 79970db | Eddie Belter | 06 July 2015, 19:05:25 UTC | Merge pull request #835 from ebelter/rt-auth-config RT Auth: use config for RT login/password | 06 July 2015, 19:05:25 UTC |
| 82f4dde | Thomas Mooney | 06 July 2015, 18:05:31 UTC | Extract DV2 dispatcher resource requirements to a configuration variable. | 06 July 2015, 18:05:31 UTC |
| bacc066 | APipe Tester | 06 July 2015, 14:56:19 UTC | updated ur submodule to eb315e1 | 06 July 2015, 14:56:19 UTC |
| 9430b6f | Thomas B. Mooney | 06 July 2015, 13:08:16 UTC | Merge pull request #843 from tmooney/cqid_forces_instrument_data_assignment CQID: Trust the configuration to know what instrument data to assign. | 06 July 2015, 13:08:16 UTC |
| ed3b70b | Eddie Belter | 03 July 2015, 18:59:35 UTC | RefCov metrics retrieval command | 03 July 2015, 18:59:35 UTC |
| 82c9b18 | APipe Tester | 03 July 2015, 12:20:10 UTC | Updated `genome` tab completion. | 03 July 2015, 12:20:10 UTC |
| 7cbad24 | Thomas Mooney | 02 July 2015, 22:32:54 UTC | aliger => aligner | 02 July 2015, 22:32:54 UTC |
| ae7a365 | Thomas Mooney | 02 July 2015, 22:01:52 UTC | Fix typo; replace "has" with a plural verb | 02 July 2015, 22:05:53 UTC |
| ef3042d | Thomas Mooney | 02 July 2015, 22:00:48 UTC | Whitespace. | 02 July 2015, 22:00:48 UTC |
| 1e9ffca | Thomas Mooney | 02 July 2015, 22:00:04 UTC | Remove old TODOs | 02 July 2015, 22:00:04 UTC |
| 32ecd74 | Feiyu Du | 02 July 2015, 21:58:49 UTC | Merge pull request #844 from dufeiyu/bug_fix Making annotation index process optional | 02 July 2015, 21:58:49 UTC |
| 255122a | Ben Ainscough | 02 July 2015, 18:22:00 UTC | Merge pull request #821 from kkrysiak/clinseq_validation_data Add options to clinseq update-analysis to use validation data as exome data | 02 July 2015, 18:22:00 UTC |
| 2345794 | Susanna Siebert | 02 July 2015, 16:54:14 UTC | Merge pull request #841 from susannasiebert/speedseq_version New speedseq freeze version using Samblaster 0.1.22 | 02 July 2015, 16:54:14 UTC |
| e2635af | Kilannin Krysiak | 02 July 2015, 16:31:29 UTC | Fixed commented text | 02 July 2015, 16:31:29 UTC |
| ac71c9b | Allison Penner Regier | 02 July 2015, 15:52:31 UTC | Merge pull request #840 from apregier/vaf-filter Add exclusive flag to vaf-filter | 02 July 2015, 15:52:31 UTC |
| 8887314 | Thomas Mooney | 02 July 2015, 15:47:39 UTC | Trust the configuration to know what instrument data to assign. | 02 July 2015, 15:47:39 UTC |
| 0b24371 | Kilannin Krysiak | 02 July 2015, 14:44:20 UTC | Merged my_trsn and validation_as_exome into 1 parameter | 02 July 2015, 14:44:20 UTC |
| 79e7d00 | APipe Tester | 02 July 2015, 12:17:48 UTC | Updated `genome` tab completion. | 02 July 2015, 12:17:48 UTC |
| b1868a2 | APipe Tester | 02 July 2015, 12:16:14 UTC | Updated class browser cache. | 02 July 2015, 12:16:14 UTC |
| f0c2b15 | Eddie Belter | 01 July 2015, 22:07:00 UTC | RT Credentials: remove default values | 01 July 2015, 22:07:00 UTC |
| ce006ba | Eddie Belter | 01 July 2015, 21:04:45 UTC | RT Auth Config: move RT URL to config | 01 July 2015, 21:04:45 UTC |
| 6edb541 | Eddie Belter | 01 July 2015, 21:02:48 UTC | RT Auth Config add default values until the puppet changes can be implemented (the new ENVs break CLE validation) | 01 July 2015, 21:02:48 UTC |
| 0e7a157 | Eddie Belter | 01 July 2015, 20:40:54 UTC | RT Auth Config: update comments | 01 July 2015, 20:40:54 UTC |
| 7bd1b9d | Eddie Belter | 01 July 2015, 20:40:02 UTC | Config: fix POD | 01 July 2015, 20:40:06 UTC |
| a84c379 | Feiyu Du | 01 July 2015, 20:18:58 UTC | Annotation index is not required since annotation_build is optional | 01 July 2015, 20:18:58 UTC |
| db39322 | Eddie Belter | 01 July 2015, 20:05:44 UTC | Merge pull request #837 from ebelter/gm GenotypeMicroarray: remove unused import_format param | 01 July 2015, 20:05:44 UTC |
| fa11dcf | Susanna Siebert | 01 July 2015, 19:59:58 UTC | Merge pull request #822 from susannasiebert/qc_framework_verify_bam_id QC tool wrappers to run verify bam id | 01 July 2015, 19:59:58 UTC |
| 5a67960 | Susanna Siebert | 01 July 2015, 17:38:10 UTC | Fix typo | 01 July 2015, 17:38:10 UTC |
| e6d9eb2 | Susanna Siebert | 29 June 2015, 20:00:53 UTC | Use new speedseq freeze version | 30 June 2015, 21:50:11 UTC |
| 7af0f9a | apregier | 30 June 2015, 18:20:13 UTC | Add exclusive flag to vaf-filter | 30 June 2015, 18:20:13 UTC |
| ef730d8 | Susanna Siebert | 29 June 2015, 16:44:46 UTC | New QC tool wrapper for samtools flagstat | 29 June 2015, 18:16:35 UTC |
| 1a7f7b2 | mkiwala | 29 June 2015, 16:49:07 UTC | Merge pull request #838 from mkiwala/genome-ptero-integration-config Set workflow_builder_backend outside of BEGIN | 29 June 2015, 16:49:07 UTC |
| a8c9c41 | Susanna Siebert | 13 April 2015, 15:57:43 UTC | Rename BamFile tool to Samtools::View | 29 June 2015, 16:16:24 UTC |
| c7d290b | Susanna Siebert | 29 June 2015, 16:16:03 UTC | Add additional flagstat metric to G::M::T::Sam::Flagstat::parse_file_into_hashref | 29 June 2015, 16:16:03 UTC |
| b06bcd4 | Susanna Siebert | 29 June 2015, 15:42:26 UTC | Add more insert size metrics | 29 June 2015, 15:42:26 UTC |
| 8a0d0cb | Michael J. Kiwala | 26 June 2015, 18:05:30 UTC | Set workflow_builder_backend outside of begin Setting 'workflow_builder_backend' inside the BEGIN block prevents the new setting from taking effect outside of the BEGIN block. Before this change, the 'workflow_builder_backend' reverted back to 'workflow', which is clearly wrong for these Ptero integration tests. This bug remained uncaught for nearly two months because of another bug. The configuration of the Genome Ptero Integration had a typo which caused the tests to only run against a particular commit of the genome repository, a commit which was from April 2015. | 26 June 2015, 18:18:01 UTC |
| e76d49e | APipe Tester | 26 June 2015, 12:18:32 UTC | Updated `genome` tab completion. | 26 June 2015, 12:18:32 UTC |
| ee0d334 | Eddie Belter | 25 June 2015, 22:38:03 UTC | GenotypeMicroarray: remove unused import_format param | 25 June 2015, 22:38:03 UTC |
| e0116f0 | Eddie Belter | 25 June 2015, 19:57:25 UTC | Merge pull request #832 from ebelter/ref-align RefAlign | 25 June 2015, 19:57:25 UTC |
| 34a3d5f | Eddie Belter | 25 June 2015, 19:43:46 UTC | Merge pull request #834 from ebelter/refseq-converter RefSeq Converter: add and use valid algorithms | 25 June 2015, 19:43:46 UTC |
| 60f27b6 | Eddie Belter | 25 June 2015, 19:25:23 UTC | Merge pull request #836 from ebelter/clin-seq CHANGELOG: bump clin-seq blessed build | 25 June 2015, 19:25:23 UTC |
| db74f0c | Eddie Belter | 24 June 2015, 19:59:23 UTC | CHANGELOG: bump clin-seq blessed build | 24 June 2015, 19:59:23 UTC |
| 348750b | Allison Penner Regier | 24 June 2015, 18:33:54 UTC | Merge pull request #829 from apregier/bedpe More tweaks to compare-bedpes | 24 June 2015, 18:33:54 UTC |
| 4fbb286 | Jason Walker | 24 June 2015, 16:46:41 UTC | Merge pull request #720 from jasonwalker80/clinseq_time_point ClinSeq caTissue Timepoint | 24 June 2015, 16:46:41 UTC |
| cdd96cc | Jason Walker | 24 June 2015, 15:51:11 UTC | Merged genome/genome master with PR720 | 24 June 2015, 15:51:11 UTC |
| 5e4c84d | apregier | 24 June 2015, 15:43:28 UTC | Error if we would overwrite a given metadata column | 24 June 2015, 15:43:28 UTC |
| 4021797 | apregier | 24 June 2015, 15:43:13 UTC | Fix doc punctuation | 24 June 2015, 15:43:13 UTC |
| 2512176 | Susanna Siebert | 24 June 2015, 13:24:38 UTC | WithVariationListVcf needs to be abstract | 24 June 2015, 13:24:38 UTC |
| 30e34c5 | APipe Tester | 24 June 2015, 12:20:45 UTC | Updated `genome` tab completion. | 24 June 2015, 12:20:45 UTC |
| ed5a3c0 | APipe Tester | 24 June 2015, 12:18:49 UTC | Updated class browser cache. | 24 June 2015, 12:18:49 UTC |
| 07ae57b | Eddie Belter | 24 June 2015, 00:17:27 UTC | RT Auth: failed model tickets command uses config for rt auth | 24 June 2015, 00:17:27 UTC |
| e6e8660 | Eddie Belter | 23 June 2015, 23:54:20 UTC | RT Login: add config for RT login and auth | 23 June 2015, 23:54:20 UTC |
| c613e74 | Eddie Belter | 23 June 2015, 23:21:38 UTC | RefSeq Converter: remove uneeded use statement | 23 June 2015, 23:21:38 UTC |
| 09dff7b | Eddie Belter | 23 June 2015, 22:39:59 UTC | RefSeq Converter: use valid values from property instead of variable | 23 June 2015, 22:39:59 UTC |
| a171e36 | Eddie Belter | 23 June 2015, 22:10:24 UTC | RefSeq Converter: add and use valid algoritms variable | 23 June 2015, 22:10:24 UTC |
| 0ee62dc | Jason Walker | 23 June 2015, 20:43:39 UTC | Updated blessed build for apipe-test-clinseq-wer | 23 June 2015, 20:43:39 UTC |
| c163e7a | Eddie Belter | 23 June 2015, 19:41:37 UTC | Merge pull request #827 from ebelter/cqid Minor CQID updates | 23 June 2015, 19:41:37 UTC |
| 6739b6b | Eddie Belter | 23 June 2015, 19:38:06 UTC | RefAlign add die when getting default model name for lane qc adn no instdata is assigned add tests | 23 June 2015, 19:38:17 UTC |
| d86057e | Eddie Belter | 23 June 2015, 19:33:21 UTC | RefAlign: update accumulated alignments directory test | 23 June 2015, 19:33:21 UTC |
| 473f3eb | Susanna Siebert | 23 June 2015, 18:19:48 UTC | Change inheritance hierarchy of G::Qc::Tool::WithVariationListVcf | 23 June 2015, 18:19:48 UTC |
| a0159b8 | Eddie Belter | 23 June 2015, 18:07:23 UTC | CQID: update skipped status message | 23 June 2015, 18:07:23 UTC |
| 9dd5a47 | Adam Coffman | 23 June 2015, 15:58:35 UTC | Merge pull request #826 from acoffman/dynamic_resource_requirements_for_align_and_merge Dynamic resource requirements for AlignAndMerge (Speedseq) | 23 June 2015, 15:58:35 UTC |
| 7d7c583 | Susanna Siebert | 23 June 2015, 15:36:09 UTC | Make variation_list_build an id_by property | 23 June 2015, 15:36:09 UTC |
| baa88c9 | Adam Coffman | 23 June 2015, 15:25:04 UTC | remove confusing reuse of "class" | 23 June 2015, 15:25:04 UTC |
| 5bf8129 | Adam Coffman | 23 June 2015, 15:22:45 UTC | define abstract subroutine with appropriate error | 23 June 2015, 15:22:45 UTC |
| e4bcd7c | Susanna Siebert | 23 June 2015, 13:53:27 UTC | Remove comment | 23 June 2015, 13:53:27 UTC |
| 27275fb | Thomas B. Mooney | 23 June 2015, 13:32:01 UTC | Merge pull request #816 from tmooney/failed_model_ticket_status New command: failed-model-ticket-status | 23 June 2015, 13:32:01 UTC |
| 5135c9b | Eddie Belter | 22 June 2015, 22:03:06 UTC | Merge pull request #830 from ebelter/gmt-validation GMT Validation: status_message | 22 June 2015, 22:03:06 UTC |
| be959f8 | Eddie Belter | 22 June 2015, 21:33:23 UTC | GMT Validation: status_message | 22 June 2015, 21:33:23 UTC |
| 4b00282 | apregier | 18 June 2015, 20:07:15 UTC | Add count of unique gold calls | 22 June 2015, 20:41:10 UTC |
| 4905e17 | apregier | 18 June 2015, 16:36:15 UTC | Flatten stats hash into the general hash | 22 June 2015, 20:41:09 UTC |
| 6356f30 | apregier | 12 June 2015, 19:42:44 UTC | Make script more flexible to pass through arbitrary metadata | 22 June 2015, 20:41:08 UTC |
| 93c23bd | Eddie Belter | 19 June 2015, 22:03:52 UTC | Merge pull request #814 from ebelter/gm-dep-cron-ref-align Genotype Microarray Dependent Cron RefAlign | 19 June 2015, 22:03:52 UTC |
| 8f259d8 | Eddie Belter | 19 June 2015, 22:01:32 UTC | Merge pull request #820 from ebelter/rm-unused-solr-scripts Remove unsed solr scripts | 19 June 2015, 22:01:32 UTC |
| baace95 | Eddie Belter | 19 June 2015, 22:01:13 UTC | Merge pull request #825 from ebelter/instdata-command-update InstData Update Command | 19 June 2015, 22:01:13 UTC |
| 1ca5eb1 | Susanna Siebert | 19 June 2015, 16:02:23 UTC | Merge pull request #824 from susannasiebert/speedseq_lsf Update speedseq to not pass number threads along as an aligner_param | 19 June 2015, 16:02:23 UTC |
| 1da9b94 | Eddie Belter | 18 June 2015, 23:41:39 UTC | RefAlign: remove complete_build_directory, update accumulated alignment s dir' | 18 June 2015, 23:42:23 UTC |
| a1a63be | Eddie Belter | 18 June 2015, 23:40:22 UTC | RefAlign Test: remove unused function | 18 June 2015, 23:40:22 UTC |
| 40f4c4c | Eddie Belter | 18 June 2015, 23:40:08 UTC | RefAlign Test: remove test of last complete build | 18 June 2015, 23:40:08 UTC |
| 18658cc | Eddie Belter | 18 June 2015, 23:39:41 UTC | RefAlign Test: use the class, get model from test factory | 18 June 2015, 23:39:41 UTC |
| 58ce0c2 | Eddie Belter | 18 June 2015, 22:44:29 UTC | CQID: use bridge __display_name__ | 18 June 2015, 22:44:29 UTC |
| 3e817a2 | Eddie Belter | 18 June 2015, 22:44:02 UTC | AnP: add __display_name__ to bridge | 18 June 2015, 22:44:02 UTC |
| 86f5e81 | Eddie Belter | 18 June 2015, 22:33:19 UTC | CQID: pass anp instdata bridge to should_skip | 18 June 2015, 22:33:19 UTC |
| 0c78596 | Eddie Belter | 18 June 2015, 22:29:57 UTC | CQID: update skip message | 18 June 2015, 22:29:57 UTC |
| 826f089 | Eddie Belter | 18 June 2015, 22:27:32 UTC | CQID: state the AnP and instdata we are working on | 18 June 2015, 22:27:32 UTC |
| 13118de | Adam Coffman | 18 June 2015, 21:47:33 UTC | remove now unused lsf requirements | 18 June 2015, 21:47:33 UTC |
| b650a45 | Adam Coffman | 18 June 2015, 21:45:46 UTC | override subs in test - we dont have a real bam file to stat | 18 June 2015, 21:45:46 UTC |
| f5aa195 | Adam Coffman | 18 June 2015, 21:44:16 UTC | populate lsf resource requirements at workflow construction | 18 June 2015, 21:44:16 UTC |
| 853bfb7 | Adam Coffman | 18 June 2015, 21:43:35 UTC | add helper method to estimate gtmp usage for speedseq | 18 June 2015, 21:43:35 UTC |
| 0210f89 | Kilannin Krysiak | 18 June 2015, 16:28:07 UTC | Added check for uninitialized | 18 June 2015, 16:28:07 UTC |
| f291f8a | Anthony Brummett | 18 June 2015, 15:32:43 UTC | Merge pull request #823 from brummett/error-message Ensure the exception message shows up in the error message. | 18 June 2015, 15:32:43 UTC |
| 5776c72 | Eddie Belter | 17 June 2015, 21:24:56 UTC | InstData Update Command remove the only_if_null to allow values to be updated expand the exclude lsit of things that shold not be eaily modifyable | 17 June 2015, 21:24:56 UTC |
| 5fe5501 | Kilannin Krysiak | 17 June 2015, 21:05:56 UTC | Replaced numeric options for my-trsn with text values | 17 June 2015, 21:05:56 UTC |
| a5282bc | Eddie Belter | 17 June 2015, 21:02:38 UTC | Merge pull request #817 from tmooney/assembly_validation_uses_new_shellcmd Assembly validation uses new shellcmd | 17 June 2015, 21:02:38 UTC |
| c0f90d2 | Adam Coffman | 17 June 2015, 20:10:06 UTC | convert name helpers to class methods | 17 June 2015, 20:10:06 UTC |
| ed57522 | Susanna Siebert | 17 June 2015, 19:27:47 UTC | Update tests to not pass along threads as an aligner param | 17 June 2015, 19:27:47 UTC |
