kfukuta/wf-transcriptomes-v202
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  • 89626ab016 Merge branch 'gene_names' into 'dev' Sam Nicholls 2026-05-22 10:23:21 +0000
  • d9c9cc6765 Add gene name to TSV outputs [CW-7160] Neil Horner 2026-05-22 10:23:21 +0000
  • a86d325393 Merge branch 'override-singularity' into 'dev' Rory Munro 2026-05-22 10:15:55 +0000
  • bfebfaa4b3 Override singularity CI Rory Munro 2026-05-22 10:15:55 +0000
  • dac0a6ef01 Merge branch 'CW-7261-b' into 'dev' Sarah Griffiths 2026-05-22 09:38:34 +0000
  • 7b94eb2ca0 Annotation quant issues test [CW-7261] Sarah Griffiths 2026-05-22 09:38:33 +0000
  • 176762fbe7 Merge branch 'alignment-outputs' into 'dev' Kiah McIntosh 2026-05-22 09:12:26 +0000
  • f5e5f3a790 Alignment outputs in per sample folder [CW-7270] Kiah McIntosh 2026-05-22 09:12:26 +0000
  • 18e0c5e92f Merge branch 'cw-7208' into 'dev' Kiah McIntosh 2026-05-21 16:19:18 +0000
  • 759cb9d868 Skip cohort processes when n=1 [CW-7208] Kiah McIntosh 2026-05-21 16:19:18 +0000
  • d520a7635b Merge branch 'CW-7265' into 'dev' Sarah Griffiths 2026-05-21 13:56:33 +0000
  • 4075523da0 Bambu always 1 thread [CW-7265] Sarah Griffiths 2026-05-21 13:56:33 +0000
  • 1dd6e3fd06 Merge branch 'no_phone_home_cw-7260' into 'dev' Neil Horner 2026-05-21 13:45:11 +0000
  • bc1ced9c9f No biocManager test phone home [CW-7260] Neil Horner 2026-05-21 13:45:11 +0000
  • e98a3f14be Merge branch 'cw-7264' into 'dev' Kiah McIntosh 2026-05-20 16:31:25 +0000
  • d124d8ba73 Sort joint bambu inputs to fix caching [CW-7264] Kiah McIntosh 2026-05-20 16:31:24 +0000
  • 38bd9ba6c0 Merge branch 'CW-7232-references' into 'dev' Natalia Garcia 2026-05-20 12:49:08 +0000
  • dc0ebf3a52 Simplify reference handling through the workflow prepareAnnotation [CW-7232] Natalia Garcia 2026-05-20 12:49:08 +0000
  • 4a3c1d1b35 Merge branch 'report_glow_up' into 'dev' Neil Horner 2026-05-20 12:31:06 +0000
  • 7194b38360 [CW-7207] Volcanic Neil Horner 2026-05-20 12:31:06 +0000
  • 3e9d57a9e1 Merge branch 'tu-ruo-next-sample-sheet' into 'dev' Natalia Garcia 2026-05-20 10:08:52 +0000
  • c3d38d9b34 Template updates (sample_sheet) Natalia Garcia 2026-05-20 10:08:52 +0000
  • c54ba7b0d7 Merge branch 'use-ruo-template' into 'dev' Natalia Garcia 2026-05-19 14:03:14 +0000
  • 779388f871 Pin wf-template@ruo-next Natalia Garcia 2026-05-19 14:03:13 +0000
  • 56ce8d2a7e Merge branch 'em1e4' into 'dev' Sam Nicholls 2026-05-19 10:04:40 +0000
  • 051e60792c
         Set conv.em to 1e-4 as documented Sam Nicholls 2026-05-19 09:29:48 +0100
  • 27f475d21a Merge branch 'cw-7250' into 'dev' Chris Wright 2026-05-18 15:14:53 +0000
  • 68809a0147 [CW-7250] fix up typography Chris Wright 2026-05-18 15:14:53 +0000
  • 0bd6f118b5 Merge branch 'cw-7210' into 'dev' Chris Wright 2026-05-18 14:14:20 +0000
  • 980d08a29a [CW-7210] Add a sample sheet reader Chris Wright 2026-05-18 14:14:19 +0000
  • 5d4009d92b Merge branch 'cw-7246' into 'dev' Kiah McIntosh 2026-05-18 12:54:01 +0000
  • e35810dcea Remove pychopper remnants [CW-7246] Kiah McIntosh 2026-05-18 12:54:01 +0000
  • a011a2dc1f Merge branch 'chunk-quant' into 'dev' Sam Nicholls 2026-05-18 12:29:48 +0000
  • db744dbe81 Scatter-gather bambu quant [CW-7201] Sam Nicholls 2026-05-18 12:29:48 +0000
  • e9b68d6222 Merge branch 'cw-7221' into 'dev' Chris Wright 2026-05-18 10:58:19 +0000
  • 8f093ed675 [CW-7221] Fix various pathological cases Chris Wright 2026-05-18 10:58:18 +0000
  • 8aa0228b21 Merge branch 'CW-7234-igv' into 'dev' Natalia Garcia 2026-05-18 09:41:50 +0000
  • 4dfd5f06e7 Restore IGV [CW-7234] Natalia Garcia 2026-05-18 09:41:49 +0000
  • 2d0ff5da08 Merge branch 'trivial' into 'dev' Chris Wright 2026-05-18 09:31:53 +0000
  • fc72470071 Merge branch 'CW-7472' into 'dev' Chris Wright 2026-05-17 11:00:25 +0000
  • aa85daafcf [CW-7472] Fix a formatting issue Chris Wright 2026-05-17 11:00:25 +0000
  • c21c609017
         Return the correct annotation Chris Wright 2026-05-16 17:02:03 +0100
  • e2166fe062 Merge branch 'cw-7235' into 'dev' Chris Wright 2026-05-16 13:22:47 +0000
  • 3d7d49795e [CW-7235] cast ? to . in gffs Chris Wright 2026-05-16 13:22:47 +0000
  • 41c5f55e2f Merge branch 'cw-7192' into 'dev' Chris Wright 2026-05-15 15:15:07 +0000
  • 31d1ffe038 [CW-7192] remove full length filtering Chris Wright 2026-05-15 15:15:07 +0000
  • 855fbb69b2 Merge branch 'cw-7241' into 'dev' Chris Wright 2026-05-14 21:48:37 +0000
  • b2be586505 [CW-7241] Fix potential issue resulting from transcript filtering Chris Wright 2026-05-14 21:48:37 +0000
  • 7278f98831 Merge branch 'ci-matrix' into 'dev' Chris Wright 2026-05-14 21:40:49 +0000
  • d4c9101e27 [CW-7231] clean up ci test matrix Chris Wright 2026-05-14 21:40:48 +0000
  • d38b7bf271 Merge branch 'arrrrrrgs' into 'dev' Chris Wright 2026-05-14 17:41:21 +0000
  • 5af948dabf [CW-7214] Tidy up CLI parsing Chris Wright 2026-05-14 17:41:21 +0000
  • a08e23849d Merge branch 'unbreak-multisample' into 'dev' Sam Nicholls 2026-05-14 17:18:57 +0000
  • 678f1de3f1 Use value channels for refs crossing samples Sam Nicholls 2026-05-14 17:18:57 +0000
  • b87c916247 Merge branch 'logfold_column_CW-7233' into 'dev' Neil Horner 2026-05-14 14:53:08 +0000
  • 1fb62d41df Rename log2Fold_contrast column [CW-7233] Neil Horner 2026-05-14 14:53:08 +0000
  • 4fa78ea462 Merge branch 'tubemap' into 'dev' Kiah McIntosh 2026-05-14 10:50:19 +0000
  • 225f9c4a44 Add tube map [CW-7218] Kiah McIntosh 2026-05-14 10:50:18 +0000
  • 42d29d3a4d Merge branch 'template-ingress' into 'dev' Sam Nicholls 2026-05-14 09:12:38 +0000
  • 06d77b2543 Use new alignment ingress [CW-7186][CW-7202][CW-7229] Sam Nicholls 2026-05-14 09:12:38 +0000
  • a99e5cda04 Merge branch 'cw-7172' into 'dev' Chris Wright 2026-05-11 09:42:54 +0000
  • f2458c5603 [CW-7172] Improve testing and reporting on differential analysis analysis Chris Wright 2026-05-11 09:42:54 +0000
  • 4e65dba188 Merge branch 'cw-7185' into 'dev' Sam Nicholls 2026-05-08 21:04:12 +0000
  • c783fdf6c6 Increase prepareAnnotationReference memory [CW-7185] Kiah McIntosh 2026-05-08 21:04:12 +0000
  • 0eb808b605 Merge branch 'CW-7191' into 'dev' Natalia Garcia 2026-05-08 14:56:31 +0000
  • d7337638f8 Add missing directives [CW-7191] Natalia Garcia 2026-05-08 14:56:31 +0000
  • 909065a298 Merge branch 'no_bioc_online_check_cw7194' into 'dev' Sam Nicholls 2026-05-08 14:08:37 +0000
  • 543b39bd79 No bioc version check [CW-7194] Neil Horner 2026-05-08 14:08:37 +0000
  • 247f1aaf0b Merge branch 'r-tests' into 'dev' Chris Wright 2026-05-08 07:55:06 +0000
  • 508a6b0525 [CW-7161] R tests Chris Wright 2026-05-08 07:55:06 +0000
  • 9ddec6ff61 Merge branch 'ref-prep' into 'dev' Kiah McIntosh 2026-05-07 10:09:36 +0000
  • 3e0dfd21e2 [CW-7166] [CW-7169] Reference and annotation preparation Chris Wright 2026-05-07 10:09:36 +0000
  • 265b462cc6 Merge branch 'de-validation-ndr-fixes' into 'dev' Chris Wright 2026-05-06 08:16:28 +0000
  • 63d9d14f17
         Fix DE validation gating and per-sample NDR Chris Wright 2026-05-05 18:42:18 +0100
  • 0633a6304d Merge branch 'r-test-infra-only' into 'dev' Chris Wright 2026-05-05 17:10:10 +0000
  • f180b9e331 [CW-7161] Add workflow-local R test infrastructure Chris Wright 2026-05-05 17:10:10 +0000
  • c17d98d6f9 Merge branch 'main-null-read-filter' into 'dev' Chris Wright 2026-05-05 16:40:24 +0000
  • 9dd5895482 Exclude ingress samples with no reads Chris Wright 2026-05-05 16:40:24 +0000
  • dcc8c04f54 Merge branch 'refresh' into 'dev' Chris Wright 2026-05-05 14:10:04 +0000
  • 43cf5bf42a Refresh workflow to use bambu, sqanti, and dexseq Chris Wright 2026-05-05 14:10:04 +0000
  • ea18f68c50 Merge branch 'update-common' into 'dev' Kiah McIntosh 2026-04-17 14:01:28 +0000
  • 057fc0e886 Update common sha Kiah McIntosh 2026-04-17 14:01:28 +0000
  • f4cae35818 Merge branch 'cjw-codex-clean' into 'dev' Chris Wright 2026-04-17 12:29:58 +0000
  • abbd3537ec Bring up to date Chris Wright 2026-04-17 12:29:57 +0000
  • c7bebf6428 Merge branch 'mr-feature' into 'dev' Kiah McIntosh 2025-12-08 14:50:51 +0000
  • 4fad6b85a8 Automated changes Chris Wright 2025-12-08 14:50:51 +0000
  • 924119c98f Merge branch 'tu-5.6.3' into 'dev' Kiah McIntosh 2025-12-05 18:16:59 +0000
  • 90e6453a8f Template update v5.6.3 [CW-6859] Kiah McIntosh 2025-12-05 18:16:58 +0000
  • 27d12e35ae Merge branch 'sgriffiths-dev-patch-45208' into 'dev' Neil Horner 2025-10-17 10:02:29 +0000
  • 01387abb63 Update CHANGELOG.md Sarah Griffiths 2025-10-17 09:57:39 +0000
  • 27b57598ef Merge branch 'tag-1.7.2' into 'dev' Neil Horner 2025-10-17 08:43:45 +0000
  • 25b88c1321 tag v1.7.2 Sarah Griffiths 2025-10-17 08:43:44 +0000
  • 297c87e92f Merge branch 'CW-6687/fix-workflow-title' into 'dev' Rory Munro 2025-10-15 15:42:28 +0000
  • 08ee6dc427
         Fix display title Rory Munro 2025-10-14 17:23:38 +0100
  • 7d5abe0c55 Merge branch 'final-tag' into 'dev' Sarah Griffiths 2025-08-01 15:02:39 +0000
  • e83c92a0e5 tag v1.7.1 Sarah Griffiths 2025-08-01 15:02:39 +0000
  • e2a7d23009 Merge branch 'sample_col_check_CW-6532' into 'dev' Neil Horner 2025-08-01 09:14:20 +0000
  • 4fe583d4ea Fix and simplify column name checking Neil Horner 2025-08-01 09:14:20 +0000
  • 7a94b2c515 Merge branch 'CW-6285' into 'dev' Sarah Griffiths 2025-07-29 08:54:20 +0000
  • 62e4266040 Output dexseq file [CW-6285] Sarah Griffiths 2025-07-29 08:54:20 +0000