Sam Nicholls
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56ce8d2a7e
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Merge branch 'em1e4' into 'dev'
Set conv.em to 1e-4 as documented
See merge request epi2melabs/workflows/wf-transcriptomes!273
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2026-05-19 10:04:40 +00:00 |
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Sam Nicholls
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051e60792c
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Set conv.em to 1e-4 as documented
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2026-05-19 09:29:48 +01:00 |
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Chris Wright
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68809a0147
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[CW-7250] fix up typography
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2026-05-18 15:14:53 +00:00 |
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Chris Wright
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980d08a29a
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[CW-7210] Add a sample sheet reader
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2026-05-18 14:14:19 +00:00 |
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Sam Nicholls
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db744dbe81
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Scatter-gather bambu quant [CW-7201]
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2026-05-18 12:29:48 +00:00 |
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Chris Wright
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8f093ed675
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[CW-7221] Fix various pathological cases
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2026-05-18 10:58:18 +00:00 |
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Chris Wright
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aa85daafcf
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[CW-7472] Fix a formatting issue
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2026-05-17 11:00:25 +00:00 |
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Chris Wright
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3d7d49795e
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[CW-7235] cast ? to . in gffs
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2026-05-16 13:22:47 +00:00 |
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Chris Wright
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31d1ffe038
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[CW-7192] remove full length filtering
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2026-05-15 15:15:07 +00:00 |
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Chris Wright
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b2be586505
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[CW-7241] Fix potential issue resulting from transcript filtering
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2026-05-14 21:48:37 +00:00 |
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Chris Wright
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5af948dabf
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[CW-7214] Tidy up CLI parsing
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2026-05-14 17:41:21 +00:00 |
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Neil Horner
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1fb62d41df
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Rename log2Fold_contrast column [CW-7233]
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2026-05-14 14:53:08 +00:00 |
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Sam Nicholls
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06d77b2543
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Use new alignment ingress [CW-7186][CW-7202][CW-7229]
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2026-05-14 09:12:38 +00:00 |
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Chris Wright
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a99e5cda04
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Merge branch 'cw-7172' into 'dev'
[CW-7172] Improve testing and reporting on differential analysis analysis
See merge request epi2melabs/workflows/wf-transcriptomes!242
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2026-05-11 09:42:54 +00:00 |
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Chris Wright
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f2458c5603
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[CW-7172] Improve testing and reporting on differential analysis analysis
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2026-05-11 09:42:54 +00:00 |
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Kiah McIntosh
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c783fdf6c6
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Increase prepareAnnotationReference memory [CW-7185]
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2026-05-08 21:04:12 +00:00 |
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Chris Wright
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508a6b0525
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[CW-7161] R tests
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2026-05-08 07:55:06 +00:00 |
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Chris Wright
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3e0dfd21e2
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[CW-7166] [CW-7169] Reference and annotation preparation
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2026-05-07 10:09:36 +00:00 |
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Chris Wright
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f180b9e331
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[CW-7161] Add workflow-local R test infrastructure
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2026-05-05 17:10:10 +00:00 |
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Chris Wright
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43cf5bf42a
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Refresh workflow to use bambu, sqanti, and dexseq
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2026-05-05 14:10:04 +00:00 |
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Chris Wright
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abbd3537ec
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Bring up to date
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2026-04-17 12:29:57 +00:00 |
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Kiah McIntosh
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90e6453a8f
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Template update v5.6.3 [CW-6859]
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2025-12-05 18:16:58 +00:00 |
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Neil Horner
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4fe583d4ea
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Fix and simplify column name checking
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2025-08-01 09:14:20 +00:00 |
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Sarah Griffiths
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62e4266040
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Output dexseq file [CW-6285]
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2025-07-29 08:54:20 +00:00 |
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Neil Horner
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b2ac1edbb9
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Container update CW-5998
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2025-05-16 08:38:28 +00:00 |
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Neil Horner
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19b54ba2ff
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Fix hyphens in sample alias CW-5484
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2025-05-14 13:55:01 +00:00 |
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Neil Horner
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18bf1d5b19
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Template update 5.6.0 [CW-6070]
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2025-05-06 10:23:01 +00:00 |
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Sarah Griffiths
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c1f784ad04
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fix memory issue by replacing seq alignment stats with flagstat [CW-5858]
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2025-03-31 09:20:35 +00:00 |
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Sarah Griffiths
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d5de051fd4
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Only use exons in DE analysis [CW-5786]
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2025-03-28 09:58:05 +00:00 |
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Sarah Griffiths
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b4bba1432b
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Template v5.5.0 updates
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2025-03-14 11:04:18 +00:00 |
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Neil Horner
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350cb8d23b
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Merge branch 'missing_file_CW-5556' into 'dev'
Fix overwritten DGE results file
See merge request epi2melabs/workflows/wf-transcriptomes!199
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2025-02-18 17:05:45 +00:00 |
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Neil Horner
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b62722751f
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Fix overwritten DGE results file
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2025-02-18 17:05:45 +00:00 |
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Kiah McIntosh
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eab8ef1efe
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Use args for R script inputs [CW-3398]
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2025-02-07 08:42:49 +00:00 |
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Neil Horner
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c8c5922965
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Access to undefined channel output bug CW-5398
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2024-12-13 11:51:04 +00:00 |
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Neil Horner
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0a5c39cdf4
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Account for stringtie multigene transcript artefacts
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2024-12-12 14:30:31 +00:00 |
|
Neil Horner
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624c16a3b1
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Update permissions
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2024-12-02 12:55:51 +00:00 |
|
Neil Horner
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5c4780a1b2
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Update report CW-3077
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2024-10-25 15:18:05 +00:00 |
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Sarah Griffiths
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d83807f38d
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Tidy de analysis
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2024-09-16 09:26:12 +00:00 |
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Sarah Griffiths
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7ced52c05b
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Template updates
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2024-09-11 12:47:01 +00:00 |
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Sam Nicholls
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46363987aa
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Output dtu_plots to local work dir then mv [CW-4886]
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2024-09-09 18:41:17 +00:00 |
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Neil Horner
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0200514536
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Remove fusion detection [CW-4552]
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2024-08-06 20:20:19 +00:00 |
|
Neil Horner
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0f4eee002a
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template update 2024-07-10
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2024-07-26 08:34:05 +00:00 |
|
Neil Horner
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c662293317
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Template update
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2024-06-27 16:13:55 +01:00 |
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Neil Horner
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e2585dcd11
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Template update 2024 05 24
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2024-05-30 19:40:11 +00:00 |
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Sarah Griffiths
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d7fcb2d5f7
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Temp update
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2024-05-10 08:42:12 +00:00 |
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Sarah Griffiths
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63e0fe6524
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change significance level to mark on MA plot
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2024-04-10 08:09:23 +00:00 |
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Sarah Griffiths
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595aae4006
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Template update
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2024-04-03 09:47:29 +00:00 |
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Sarah Griffiths
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6a14a1d85b
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Remove need to retry based on GTF/GFF
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2024-02-22 09:34:38 +00:00 |
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Sarah Griffiths
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e3b1967872
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Improve ref annotation transcript id version handling
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2024-02-19 10:29:04 +00:00 |
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Sarah Griffiths
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e30d3aec98
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DE_analysis params change input types to numeric
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2024-02-16 10:23:15 +00:00 |
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