kfukuta/wf-transcriptomes-v202
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  • f104de8caf Merge branch 'v202' into 'dev' main v2.0.2 Sam Nicholls 2026-07-14 12:52:05 +0000
  • 38cb7351da wf-transcriptomes v2.0.2 Sam Nicholls 2026-07-14 12:52:05 +0000
  • a76531637e Merge branch 'dtype_samples_CW-7394' into 'dev' Neil Horner 2026-07-14 11:48:48 +0000
  • 725768cebb Enforce str dtype for sample metadata [CW-7394] Neil Horner 2026-07-14 11:48:48 +0000
  • 2be3c50d33 Merge branch 'mods_exist_CW-7416' into 'dev' Neil Horner 2026-07-14 10:05:38 +0000
  • 205ba78998 Test for mods output [CW-7416] Neil Horner 2026-07-14 10:05:38 +0000
  • d81d0cbe9c Merge branch 'cw-7421' into 'dev' Sam Nicholls 2026-07-14 09:54:50 +0000
  • 59f6db51bb Add 2'-O-* mod_code labels [CW-7421] Sam Nicholls 2026-07-14 09:54:50 +0000
  • 66b0e377a9 Merge branch 'cw-7391' into 'dev' Sam Nicholls 2026-07-13 16:00:41 +0000
  • 4613584c69 Improve messaging for seqnames with no transcript records [CW-7391] Sam Nicholls 2026-07-13 16:00:41 +0000
  • c09fa66ffc Merge branch 'CW-7387' into 'dev' Sarah Griffiths 2026-07-10 09:54:05 +0000
  • 66655043ea Remove analysis_group mention [CW-7387] Sarah Griffiths 2026-07-10 09:54:04 +0000
  • d3d2a15efd Merge branch 'uf_wrong_CW-7384' into 'dev' Neil Horner 2026-07-08 11:41:38 +0000
  • 8f863575c0 Use -ub for cDNA [CW-7384] Neil Horner 2026-07-08 11:41:37 +0000
  • 3040c2796c Merge branch 'v201-changelog' into 'dev' Sam Nicholls 2026-06-18 09:12:55 +0000
  • bac1638b49 wf-transcriptomics 2.0.1 Sam Nicholls 2026-06-18 09:12:55 +0000
  • 50fd84597d Merge branch 'yaxisrange_CW-7354' into 'dev' Neil Horner 2026-06-18 08:34:14 +0000
  • 58b8582ea5 Volcano ylim slider [CW-7354] Neil Horner 2026-06-18 08:34:14 +0000
  • cca505faae Merge branch 'cw-7337' into 'dev' Sam Nicholls 2026-06-17 10:42:21 +0000
  • 960ddbfc46 Stream collate RDS to reduce max mem [CW-7337] Sam Nicholls 2026-06-17 10:42:20 +0000
  • f698102333 Merge branch 'CW-7332' into 'dev' Natalia Garcia 2026-06-16 14:25:44 +0000
  • cd575b9fcb IGV tracks mismatch index when there is one BAM per sample [CW-7332,CW-7349] Natalia Garcia 2026-06-16 14:25:43 +0000
  • 13ce17c631 Merge branch 'na_volcano_CW-7345' into 'dev' Neil Horner 2026-06-16 13:02:23 +0000
  • 2ed160cbe7 Volcano filter NA [CW-7345] Neil Horner 2026-06-16 13:02:23 +0000
  • a30eaf2ffc Merge branch 'scinot_CW-7342' into 'dev' Neil Horner 2026-06-16 10:17:59 +0000
  • c99ba8cd9f Sci format for volcano padj values [CW-7342] Neil Horner 2026-06-16 10:17:59 +0000
  • 0aa3ce3cad Merge branch 'cw-7338' into 'dev' Sam Nicholls 2026-06-15 13:38:03 +0000
  • 760ffa009e Chunk RDS from disk if provided a path [CW-7338] Sam Nicholls 2026-06-15 13:38:02 +0000
  • 3d04f3485a Merge branch 'cw-7333' into 'dev' Sam Nicholls 2026-06-12 16:03:48 +0000
  • 6099173238 Handle full join fail during bambu quant [CW-7333] Sam Nicholls 2026-06-12 16:03:48 +0000
  • 94823e73d1 Use xlarge-highio Sam Nicholls 2026-06-09 12:08:19 +0000
  • fbb1529816 Use smoke_de as default CI test Sam Nicholls 2026-06-09 12:04:53 +0000
  • 1fa032ae0e Merge branch 'v200-rc2' into 'dev' Sam Nicholls 2026-06-09 11:58:17 +0000
  • c21588761b wf-transcriptomes v2.0.0 Sam Nicholls 2026-06-09 11:58:17 +0000
  • f1dbc69191 Merge branch 'v2releasechanglog' into 'dev' Sam Nicholls 2026-05-28 10:54:50 +0000
  • d7a0e96a44 wf-transcriptomes 2.0.0-rc1 Harrison Pirt 2026-05-28 10:54:49 +0000
  • 0b7dbdb294 Merge branch 'devon-docs' into 'dev' Neil Horner 2026-05-28 10:21:37 +0000
  • 957e57d87b Final README pass Chris Wright 2026-05-28 10:21:37 +0000
  • 274548f64f Merge branch 'remove_demo' into 'dev' Sam Nicholls 2026-05-28 07:15:20 +0000
  • 30a9880bf7 Remove demo data to avoid breaking production demo Sarah Griffiths 2026-05-28 07:15:20 +0000
  • 334173d613 Merge branch 'report-explain' into 'dev' Sarah Griffiths 2026-05-27 16:17:22 +0000
  • e17fec8bc0 Add brief description to each section in report Sarah Griffiths 2026-05-27 16:17:22 +0000
  • 0129592acc Merge branch 'tidy-params' into 'dev' Sarah Griffiths 2026-05-27 15:40:53 +0000
  • bca0f01bf6 Tidy params Sam Nicholls 2026-05-27 15:40:53 +0000
  • 26d830a916 Merge branch 'condition_report_fix' into 'dev' Neil Horner 2026-05-27 15:05:18 +0000
  • 3e53b755cc Condition report fix [CW-7283] Neil Horner 2026-05-27 15:05:18 +0000
  • 541de0c1f9 Merge branch 'stop-demo-release' into 'dev' Sarah Griffiths 2026-05-27 14:37:54 +0000
  • ef08219e11 Avoid publishing demo for transcriptomes Sarah Griffiths 2026-05-27 14:37:53 +0000
  • 10b2013b6a Merge branch 'transcriptome_table_order' into 'dev' Neil Horner 2026-05-27 13:20:41 +0000
  • 722d736f24 Report minor fixes [CW-7281] Neil Horner 2026-05-27 13:20:41 +0000
  • 9cba80832d Merge branch 'unnecessary-igv' into 'dev' Sam Nicholls 2026-05-27 12:24:08 +0000
  • 262f49944e Publish refs for IGV only when necessary [CW-7280] Sam Nicholls 2026-05-27 12:24:07 +0000
  • c96be955b5 Merge branch 'template-updates-sorting' into 'dev' Natalia Garcia 2026-05-27 11:59:12 +0000
  • 531975c004 Template updates: sort threads param Natalia Garcia 2026-05-27 11:59:11 +0000
  • d73b9a2721 Merge branch 'template-updates2' into 'dev' Natalia Garcia 2026-05-27 10:00:41 +0000
  • 9d59c6b902 Template updates: reference Natalia Garcia 2026-05-27 10:00:40 +0000
  • 33ad57cdaa Merge branch 'CW-7279' into 'dev' Natalia Garcia 2026-05-27 09:29:30 +0000
  • 7e301319fc Use mode copy in publishDir [CW-7279] Natalia Garcia 2026-05-27 09:29:30 +0000
  • dda764f48c Merge branch 'cw-7196-b' into 'dev' Sam Nicholls 2026-05-27 08:11:02 +0000
  • 4bc3cf727f Per-sample mod summary Sam Nicholls 2026-05-27 08:11:02 +0000
  • 9d684eeb29 Merge branch 'use-extra-validation' into 'dev' Natalia Garcia 2026-05-27 08:10:04 +0000
  • 0ae50f9a35 Check is a valid sample sheet use the extensive validation [CW-7210] Natalia Garcia 2026-05-27 08:10:04 +0000
  • 74cbe196b2 Merge branch 'fix-ci-test-2' into 'dev' Sam Nicholls 2026-05-26 20:12:45 +0000
  • b6f9efd9ae Restore modkit test with smaller gtf, fix join error Sam Nicholls 2026-05-26 20:12:45 +0000
  • e28be80e1a Merge branch 'shorter-names' into 'dev' Sam Nicholls 2026-05-26 20:12:38 +0000
  • efbe4d007c Shorten workflow names for log Sam Nicholls 2026-05-26 20:12:38 +0000
  • e95b51016a Merge branch 'tidy-up-schema-validation' into 'dev' Natalia Garcia 2026-05-26 18:42:12 +0000
  • 6ca2f2f027 Tidy up schema validation [CW-7278] Natalia Garcia 2026-05-26 18:42:11 +0000
  • abf467e528 Merge branch '20_volcano_points_cw-7277' into 'dev' Neil Horner 2026-05-26 17:12:20 +0000
  • 01e8652317 Use all point for volcano and tables [CW-7277] Neil Horner 2026-05-26 17:12:20 +0000
  • da5f78497e Merge branch 'hier_low_data_cw-7275' into 'dev' Neil Horner 2026-05-26 17:10:46 +0000
  • fa884c71c1 Clustering plots low data [CW-7275] Neil Horner 2026-05-26 17:10:46 +0000
  • a4b08414cb Merge branch 'remove-bigwig' into 'dev' Rory Munro 2026-05-26 16:43:06 +0000
  • 1192f09bc7 Remove bigwig CI test Rory Munro 2026-05-26 16:43:05 +0000
  • c36404422e Merge branch 'CW-7274' into 'dev' Sarah Griffiths 2026-05-26 14:44:50 +0000
  • 3ca4511b5b Add force alignment option [CW-7274] Sarah Griffiths 2026-05-26 14:44:50 +0000
  • 6e72a4538c Merge branch 'rmunro-dev-patch-42566' into 'dev' Rory Munro 2026-05-26 12:31:05 +0000
  • 86d100c869 Bump modkit sha version [CW-7273] Rory Munro 2026-05-26 12:31:05 +0000
  • 3d49d01ff2 Merge branch 'tube-map-update' into 'dev' Kiah McIntosh 2026-05-26 12:27:16 +0000
  • dff1353790 Tube map update Kiah McIntosh 2026-05-26 12:27:15 +0000
  • 6327eda710 Merge branch 'cw-7196' into 'dev' Sam Nicholls 2026-05-26 09:52:39 +0000
  • 175e6c9437 Per-sample pileup counts [CW-7196] Sam Nicholls 2026-05-26 09:52:38 +0000
  • c2656983d8 Merge branch 'exclude-data-artifacts' into 'dev' Sam Nicholls 2026-05-26 08:04:59 +0000
  • 6c0a59581f CI : Exclude downloaded data artifacts Sam Nicholls 2026-05-26 08:04:59 +0000
  • c87a5ce09c Merge branch 'CW-7212' into 'dev' Natalia Garcia 2026-05-26 07:53:34 +0000
  • 04ddfbf872 Exclude non existent samples or samples without reads after ingress Natalia Garcia 2026-05-26 07:53:34 +0000
  • d416441e11 Merge branch 'CW-7271_missing_summary' into 'dev' Sarah Griffiths 2026-05-22 17:05:56 +0000
  • 020d555219 Add the missing annotation ref summary [CW-7271] Neil Horner 2026-05-22 17:05:56 +0000
  • a5c25ec0a1 Merge branch 'tube-map-modkit' into 'dev' Kiah McIntosh 2026-05-22 16:33:01 +0000
  • df2d333797 Add modkit to tube map Kiah McIntosh 2026-05-22 16:33:01 +0000
  • 50b971604e Merge branch 'cw-7238' into 'dev' Kiah McIntosh 2026-05-22 15:28:21 +0000
  • 1f456da61d SQANTI3 results in report [CW-7238] Kiah McIntosh 2026-05-22 15:28:21 +0000
  • 845c03f7f5 Merge branch 'hier_plots' into 'dev' Neil Horner 2026-05-22 14:34:50 +0000
  • 5823f04809 [CW-7211] Hierarchical plot + PCA Neil Horner 2026-05-22 14:34:50 +0000
  • 3204d24045 Merge branch 'template-updates' into 'dev' Natalia Garcia 2026-05-22 12:58:17 +0000
  • 2cfc7b2549 Use new sample sheet validation Natalia Garcia 2026-05-22 12:58:17 +0000
  • 1b3155d591 Merge branch 'report_glow_up_2' into 'dev' Neil Horner 2026-05-22 11:55:44 +0000
  • f45056c438 Report glow up 2 [CW-7207] Neil Horner 2026-05-22 11:55:44 +0000
  • 8c6196ddc1 Merge branch 'cw-7270-readme' into 'dev' Kiah McIntosh 2026-05-22 10:44:40 +0000
  • 90cc4cf73b Update readme for alignment and ingress outputs [CW-7270] Kiah McIntosh 2026-05-22 10:44:40 +0000