Neil Horner
f45056c438
Report glow up 2 [CW-7207]
2026-05-22 11:55:44 +00:00
Neil Horner
d9c9cc6765
Add gene name to TSV outputs [CW-7160]
2026-05-22 10:23:21 +00:00
Sarah Griffiths
7b94eb2ca0
Annotation quant issues test [CW-7261]
2026-05-22 09:38:33 +00:00
Kiah McIntosh
759cb9d868
Skip cohort processes when n=1 [CW-7208]
2026-05-21 16:19:18 +00:00
Sarah Griffiths
d520a7635b
Merge branch 'CW-7265' into 'dev'
...
Bambu always 1 thread [CW-7265]
Closes CW-7265
See merge request epi2melabs/workflows/wf-transcriptomes!285
2026-05-21 13:56:33 +00:00
Sarah Griffiths
4075523da0
Bambu always 1 thread [CW-7265]
2026-05-21 13:56:33 +00:00
Neil Horner
1dd6e3fd06
Merge branch 'no_phone_home_cw-7260' into 'dev'
...
No biocManager test phone home [CW-7260]
See merge request epi2melabs/workflows/wf-transcriptomes!277
2026-05-21 13:45:11 +00:00
Neil Horner
bc1ced9c9f
No biocManager test phone home [CW-7260]
2026-05-21 13:45:11 +00:00
Natalia Garcia
38bd9ba6c0
Merge branch 'CW-7232-references' into 'dev'
...
Simplify reference handling through the workflow prepareAnnotation [CW-7232]
Closes CW-7232
See merge request epi2melabs/workflows/wf-transcriptomes!275
2026-05-20 12:49:08 +00:00
Natalia Garcia
dc0ebf3a52
Simplify reference handling through the workflow prepareAnnotation [CW-7232]
2026-05-20 12:49:08 +00:00
Neil Horner
7194b38360
[CW-7207] Volcanic
2026-05-20 12:31:06 +00:00
Natalia Garcia
c3d38d9b34
Template updates (sample_sheet)
2026-05-20 10:08:52 +00:00
Sam Nicholls
56ce8d2a7e
Merge branch 'em1e4' into 'dev'
...
Set conv.em to 1e-4 as documented
See merge request epi2melabs/workflows/wf-transcriptomes!273
2026-05-19 10:04:40 +00:00
Sam Nicholls
051e60792c
Set conv.em to 1e-4 as documented
2026-05-19 09:29:48 +01:00
Chris Wright
68809a0147
[CW-7250] fix up typography
2026-05-18 15:14:53 +00:00
Chris Wright
980d08a29a
[CW-7210] Add a sample sheet reader
2026-05-18 14:14:19 +00:00
Sam Nicholls
db744dbe81
Scatter-gather bambu quant [CW-7201]
2026-05-18 12:29:48 +00:00
Chris Wright
8f093ed675
[CW-7221] Fix various pathological cases
2026-05-18 10:58:18 +00:00
Chris Wright
aa85daafcf
[CW-7472] Fix a formatting issue
2026-05-17 11:00:25 +00:00
Chris Wright
3d7d49795e
[CW-7235] cast ? to . in gffs
2026-05-16 13:22:47 +00:00
Chris Wright
31d1ffe038
[CW-7192] remove full length filtering
2026-05-15 15:15:07 +00:00
Chris Wright
b2be586505
[CW-7241] Fix potential issue resulting from transcript filtering
2026-05-14 21:48:37 +00:00
Chris Wright
5af948dabf
[CW-7214] Tidy up CLI parsing
2026-05-14 17:41:21 +00:00
Neil Horner
1fb62d41df
Rename log2Fold_contrast column [CW-7233]
2026-05-14 14:53:08 +00:00
Sam Nicholls
06d77b2543
Use new alignment ingress [CW-7186][CW-7202][CW-7229]
2026-05-14 09:12:38 +00:00
Chris Wright
a99e5cda04
Merge branch 'cw-7172' into 'dev'
...
[CW-7172] Improve testing and reporting on differential analysis analysis
See merge request epi2melabs/workflows/wf-transcriptomes!242
2026-05-11 09:42:54 +00:00
Chris Wright
f2458c5603
[CW-7172] Improve testing and reporting on differential analysis analysis
2026-05-11 09:42:54 +00:00
Kiah McIntosh
c783fdf6c6
Increase prepareAnnotationReference memory [CW-7185]
2026-05-08 21:04:12 +00:00
Chris Wright
508a6b0525
[CW-7161] R tests
2026-05-08 07:55:06 +00:00
Chris Wright
3e0dfd21e2
[CW-7166] [CW-7169] Reference and annotation preparation
2026-05-07 10:09:36 +00:00
Chris Wright
f180b9e331
[CW-7161] Add workflow-local R test infrastructure
2026-05-05 17:10:10 +00:00
Chris Wright
43cf5bf42a
Refresh workflow to use bambu, sqanti, and dexseq
2026-05-05 14:10:04 +00:00
Chris Wright
abbd3537ec
Bring up to date
2026-04-17 12:29:57 +00:00
Kiah McIntosh
90e6453a8f
Template update v5.6.3 [CW-6859]
2025-12-05 18:16:58 +00:00
Neil Horner
4fe583d4ea
Fix and simplify column name checking
2025-08-01 09:14:20 +00:00
Sarah Griffiths
62e4266040
Output dexseq file [CW-6285]
2025-07-29 08:54:20 +00:00
Neil Horner
b2ac1edbb9
Container update CW-5998
2025-05-16 08:38:28 +00:00
Neil Horner
19b54ba2ff
Fix hyphens in sample alias CW-5484
2025-05-14 13:55:01 +00:00
Neil Horner
18bf1d5b19
Template update 5.6.0 [CW-6070]
2025-05-06 10:23:01 +00:00
Sarah Griffiths
c1f784ad04
fix memory issue by replacing seq alignment stats with flagstat [CW-5858]
2025-03-31 09:20:35 +00:00
Sarah Griffiths
d5de051fd4
Only use exons in DE analysis [CW-5786]
2025-03-28 09:58:05 +00:00
Sarah Griffiths
b4bba1432b
Template v5.5.0 updates
2025-03-14 11:04:18 +00:00
Neil Horner
350cb8d23b
Merge branch 'missing_file_CW-5556' into 'dev'
...
Fix overwritten DGE results file
See merge request epi2melabs/workflows/wf-transcriptomes!199
2025-02-18 17:05:45 +00:00
Neil Horner
b62722751f
Fix overwritten DGE results file
2025-02-18 17:05:45 +00:00
Kiah McIntosh
eab8ef1efe
Use args for R script inputs [CW-3398]
2025-02-07 08:42:49 +00:00
Neil Horner
c8c5922965
Access to undefined channel output bug CW-5398
2024-12-13 11:51:04 +00:00
Neil Horner
0a5c39cdf4
Account for stringtie multigene transcript artefacts
2024-12-12 14:30:31 +00:00
Neil Horner
624c16a3b1
Update permissions
2024-12-02 12:55:51 +00:00
Neil Horner
5c4780a1b2
Update report CW-3077
2024-10-25 15:18:05 +00:00
Sarah Griffiths
d83807f38d
Tidy de analysis
2024-09-16 09:26:12 +00:00
