kfukuta/wf-transcriptomes-v202
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  • a9e63518e5 Merge branch 'CW-6125' into 'dev' Sarah Griffiths 2025-06-20 08:43:15 +0000
  • 85b767358c Filter out unstranded annotations and log warning [CW-6125] Sarah Griffiths 2025-06-20 08:43:15 +0000
  • 9f18c3f0d5 Merge branch 'container_update_CW-5998' into 'dev' Neil Horner 2025-05-16 08:38:28 +0000
  • b2ac1edbb9 Container update CW-5998 Neil Horner 2025-05-16 08:38:28 +0000
  • 2df9061a48 Merge branch 'alias_hyphens_CW-5484' into 'dev' Neil Horner 2025-05-14 13:55:02 +0000
  • 19b54ba2ff Fix hyphens in sample alias CW-5484 Neil Horner 2025-05-14 13:55:01 +0000
  • bb47d92ac2 Merge branch 'TU_5.6.1' into 'dev' Neil Horner 2025-05-09 07:05:35 +0000
  • c84a197da5 Tu 5.6.1 [CW-6099] Neil Horner 2025-05-09 07:05:34 +0000
  • 1b3f49a1ac Merge branch 'template_update_5.6.0' into 'dev' Neil Horner 2025-05-06 10:23:01 +0000
  • 18bf1d5b19 Template update 5.6.0 [CW-6070] Neil Horner 2025-05-06 10:23:01 +0000
  • a74a34763e Merge branch 'memory_mac_ci' into 'dev' Sarah Griffiths 2025-04-15 11:20:42 +0000
  • 11c9221edc memory ci config Sarah Griffiths 2025-04-15 11:20:42 +0000
  • 1d76e7326e Merge branch 'CW-5950' into 'dev' Sarah Griffiths 2025-04-11 13:22:49 +0000
  • 00c2e9a18b Fix aws/docker demo cmd [CW-5950] Sarah Griffiths 2025-04-11 13:22:48 +0000
  • cd97c1398e Merge branch 'CW-5911' into 'dev' Sarah Griffiths 2025-04-03 12:57:58 +0000
  • 390739cf8a Output BAMS in all cases apart from transcriptome-source precomputed [CW-5911] Sarah Griffiths 2025-04-03 12:57:58 +0000
  • 6f91cf59b1 Merge branch 'CW-5858' into 'dev' Sarah Griffiths 2025-03-31 09:20:36 +0000
  • c1f784ad04 fix memory issue by replacing seq alignment stats with flagstat [CW-5858] Sarah Griffiths 2025-03-31 09:20:35 +0000
  • 60ec205339 Merge branch 'CW-5786' into 'dev' Sarah Griffiths 2025-03-28 09:58:05 +0000
  • d5de051fd4 Only use exons in DE analysis [CW-5786] Sarah Griffiths 2025-03-28 09:58:05 +0000
  • 9900143122 Merge branch 'CW-2965' into 'dev' Sarah Griffiths 2025-03-14 19:06:47 +0000
  • f9bd2ab574 Error message if ref_genome and ref_annotation mismatch CW-2965 Sarah Griffiths 2025-03-14 19:06:47 +0000
  • 9ecd1345e9 Merge branch 'temp-update' into 'dev' Neil Horner 2025-03-14 11:04:19 +0000
  • b4bba1432b Template v5.5.0 updates Sarah Griffiths 2025-03-14 11:04:18 +0000
  • 9701041ce5 Merge branch 'fixup-docs' into 'dev' Chris Wright 2025-03-04 18:20:49 +0000
  • d2c1db81e8
         remove spaces in {{ ref_genome file }} in docs Chris Wright 2025-03-04 16:24:06 +0000
  • 350cb8d23b Merge branch 'missing_file_CW-5556' into 'dev' Neil Horner 2025-02-18 17:05:45 +0000
  • b62722751f Fix overwritten DGE results file Neil Horner 2025-02-18 17:05:45 +0000
  • 205ff5ca59 Merge branch 'cw-5563-wf-transcriptomes' into 'dev' Natalia Garcia 2025-02-13 23:39:09 +0000
  • 122ad8403a Update workflow tags [CW-5563] Natalia Garcia 2025-02-13 23:39:09 +0000
  • 428e337e22 Merge branch 'cw-3398' into 'dev' Kiah McIntosh 2025-02-07 08:42:49 +0000
  • eab8ef1efe Use args for R script inputs [CW-3398] Kiah McIntosh 2025-02-07 08:42:49 +0000
  • 91a514abd2 Merge branch 'schema_updates_CW-5529' into 'dev' Neil Horner 2025-01-23 10:59:32 +0000
  • e534921877 Update schema Neil Horner 2025-01-23 10:59:31 +0000
  • 632a8f85a2 Merge branch 'split_bam_mem_CW-5352' into 'dev' Matt Parker 2025-01-03 17:06:38 +0000
  • 937a41f2cc Update memory for split_bam and build_minimap_index_transcriptome Neil Horner 2025-01-03 17:06:38 +0000
  • a33f3b967c Merge branch 'bump_v1.6.1' into 'dev' Matt Parker 2025-01-03 12:44:09 +0000
  • 39ef6ab16a bump version Neil Horner 2025-01-03 12:44:08 +0000
  • 724a6515ea Merge branch 'empty_gff_CW-5438' into 'dev' Neil Horner 2024-12-18 15:01:34 +0000
  • 0ec44d03bd Empty GFF bug CW-5438 Neil Horner 2024-12-18 15:01:33 +0000
  • 74c19f1ea5 Merge branch 'bump_v1.6.0' into 'dev' Matt Parker 2024-12-13 13:11:56 +0000
  • 7ca3110648 Bump V1.6.0 Neil Horner 2024-12-13 13:11:56 +0000
  • cb00ede5d8 Merge branch 'CW-5398' into 'dev' Neil Horner 2024-12-13 11:51:07 +0000
  • c8c5922965 Access to undefined channel output bug CW-5398 Neil Horner 2024-12-13 11:51:04 +0000
  • 4c46f88f00 Merge branch 'gene_assignment_CW-5416' into 'dev' Neil Horner 2024-12-12 14:30:32 +0000
  • 0a5c39cdf4 Account for stringtie multigene transcript artefacts Neil Horner 2024-12-12 14:30:31 +0000
  • 112e87ad94 Merge branch 'template_2024_12_02' into 'dev' Neil Horner 2024-12-05 10:26:26 +0000
  • d38c7f3661 template update Neil Horner 2024-12-05 10:26:25 +0000
  • 474c0fae3b Merge branch 'template_update_dec24' into 'dev' Neil Horner 2024-12-02 12:55:51 +0000
  • 624c16a3b1 Update permissions Neil Horner 2024-12-02 12:55:51 +0000
  • b3fbb1117c Merge branch 'CW-3930' into 'dev' Sarah Griffiths 2024-11-05 11:51:40 +0000
  • 465d060933 Actually output the dexseq file Sarah Griffiths 2024-11-05 11:51:40 +0000
  • 45a717aaf3 Merge branch 'bokehreport_CW-3077' into 'dev' Neil Horner 2024-10-25 15:18:05 +0000
  • 5c4780a1b2 Update report CW-3077 Neil Horner 2024-10-25 15:18:05 +0000
  • d2ddad27a2 Merge branch 'CW-4886' into 'dev' Sarah Griffiths 2024-09-16 09:26:13 +0000
  • d83807f38d Tidy de analysis Sarah Griffiths 2024-09-16 09:26:12 +0000
  • beb094ea85 Merge branch 'CW-4613-b' into 'dev' Sam Nicholls 2024-09-13 11:48:16 +0000
  • be1d322287 IGV absolute paths fix Sarah Griffiths 2024-09-13 11:48:16 +0000
  • ce4bfa9a30 Merge branch 'template-updates' into 'dev' Sarah Griffiths 2024-09-11 12:47:01 +0000
  • 7ced52c05b Template updates Sarah Griffiths 2024-09-11 12:47:01 +0000
  • 31085d0fe4 Merge branch 'cw-4886' into 'dev' Sam Nicholls 2024-09-09 18:41:18 +0000
  • 46363987aa Output dtu_plots to local work dir then mv [CW-4886] Sam Nicholls 2024-09-09 18:41:17 +0000
  • f8e08baed1 Merge branch 'CW-4613' into 'dev' Sarah Griffiths 2024-09-06 09:27:56 +0000
  • 14fe76dabc CW-4613 IGV config Sarah Griffiths 2024-09-06 09:27:56 +0000
  • 7287fdcdb1 Merge branch 'v1.3.0_fix' into 'dev' Neil Horner 2024-08-08 13:43:26 +0000
  • f62ec6c127 Missed v from version Neil Horner 2024-08-08 13:08:59 +0100
  • d7bb5c80f7 Merge branch 'pychopper_primer_CW_4184' into 'dev' Neil Horner 2024-08-07 11:31:15 +0000
  • abc40d9015 Add new cDNA kits Neil Horner 2024-08-07 11:31:14 +0000
  • 40456d676b Merge branch 'remove_jaffal_CW-4552' into 'dev' Sam Nicholls 2024-08-06 20:20:20 +0000
  • 0200514536 Remove fusion detection [CW-4552] Neil Horner 2024-08-06 20:20:19 +0000
  • a037538744 Merge branch 'template_2024-07-10' into 'dev' Sam Nicholls 2024-07-26 08:34:05 +0000
  • 0f4eee002a template update 2024-07-10 Neil Horner 2024-07-26 08:34:05 +0000
  • f01006c302 Merge branch 'v1.2.1' into 'dev' Neil Horner 2024-07-04 14:48:31 +0000
  • a5699b2945 Bump v1.2.1 Neil Horner 2024-07-04 14:48:30 +0000
  • 3d5c4c38eb Merge branch 'template_update_0624' into 'dev' Neil Horner 2024-07-04 13:25:20 +0000
  • c662293317 Template update Neil Horner 2024-06-27 16:13:55 +0100
  • 1fed562746 Merge branch 'pychop_threads_CW-4010' into 'dev' Neil Horner 2024-06-25 14:11:28 +0000
  • 411290d5a4 Give pychopper more threads Neil Horner 2024-06-25 14:11:28 +0000
  • d5df11cce4 Merge branch 'CW-3998' into 'dev' Sarah Griffiths 2024-06-25 13:08:32 +0000
  • 57c0f5b303 Handle annotations with no strand CW-3998 Sarah Griffiths 2024-06-25 13:08:32 +0000
  • 9353e23cc9 Merge branch 'bump_v1.2.0' into 'dev' Sam Nicholls 2024-06-04 17:28:29 +0000
  • 515c8c0ed8 Bump v1.2.0 Neil Horner 2024-06-04 17:28:29 +0000
  • f89a61d304 Merge branch 'bams_CW-3512' into 'dev' Neil Horner 2024-06-04 09:25:35 +0000
  • cfa41f16d0 BAM input CW-3512 Neil Horner 2024-06-04 09:25:31 +0000
  • 7ca0d269f4 Merge branch 'template_2024-05-24' into 'dev' Natalia Garcia 2024-05-30 19:40:11 +0000
  • e2585dcd11 Template update 2024 05 24 Neil Horner 2024-05-30 19:40:11 +0000
  • 39cc58ae9e Merge branch 'temp-update' into 'dev' Sam Nicholls 2024-05-10 08:42:13 +0000
  • d7fcb2d5f7 Temp update Sarah Griffiths 2024-05-10 08:42:12 +0000
  • 6f2ac3241b Merge branch 'CW-3244' into 'dev' Sarah Griffiths 2024-04-10 08:09:23 +0000
  • 63e0fe6524 change significance level to mark on MA plot Sarah Griffiths 2024-04-10 08:09:23 +0000
  • f85e039f98 Merge branch 'template-update' into 'dev' Sarah Griffiths 2024-04-03 09:47:30 +0000
  • 595aae4006 Template update Sarah Griffiths 2024-04-03 09:47:29 +0000
  • 999fb4e44a Merge branch 'tag' into 'dev' Sarah Griffiths 2024-03-05 11:47:23 +0000
  • bd5c89efc5 Tag v1.1.1 Sarah Griffiths 2024-03-05 11:47:23 +0000
  • 914c4a0c58 Merge branch 'CW-3516' into 'dev' Sarah Griffiths 2024-02-22 09:34:39 +0000
  • 6a14a1d85b Remove need to retry based on GTF/GFF Sarah Griffiths 2024-02-22 09:34:38 +0000
  • 05b3f3363b Merge branch 'CW-3532' into 'dev' Sam Nicholls 2024-02-19 10:29:04 +0000
  • e3b1967872 Improve ref annotation transcript id version handling Sarah Griffiths 2024-02-19 10:29:04 +0000
  • f3e2c964f3 Merge branch 'CW-3464' into 'dev' Matt Parker 2024-02-16 10:23:15 +0000
  • e30d3aec98 DE_analysis params change input types to numeric Sarah Griffiths 2024-02-16 10:23:15 +0000