Neil Horner
c99ba8cd9f
Sci format for volcano padj values [CW-7342]
2026-06-16 10:17:59 +00:00
Sam Nicholls
760ffa009e
Chunk RDS from disk if provided a path [CW-7338]
2026-06-15 13:38:02 +00:00
Sam Nicholls
6099173238
Handle full join fail during bambu quant [CW-7333]
2026-06-12 16:03:48 +00:00
Sam Nicholls
c21588761b
wf-transcriptomes v2.0.0
2026-06-09 11:58:17 +00:00
Sarah Griffiths
e17fec8bc0
Add brief description to each section in report
2026-05-27 16:17:22 +00:00
Neil Horner
3e53b755cc
Condition report fix [CW-7283]
2026-05-27 15:05:18 +00:00
Neil Horner
722d736f24
Report minor fixes [CW-7281]
2026-05-27 13:20:41 +00:00
Sam Nicholls
dda764f48c
Merge branch 'cw-7196-b' into 'dev'
...
Per-sample mod summary
See merge request epi2melabs/workflows/wf-transcriptomes!294
2026-05-27 08:11:02 +00:00
Sam Nicholls
4bc3cf727f
Per-sample mod summary
2026-05-27 08:11:02 +00:00
Natalia Garcia
0ae50f9a35
Check is a valid sample sheet use the extensive validation [CW-7210]
2026-05-27 08:10:04 +00:00
Neil Horner
abf467e528
Merge branch '20_volcano_points_cw-7277' into 'dev'
...
Use all point for volcano and tables [CW-7277]
See merge request epi2melabs/workflows/wf-transcriptomes!300
2026-05-26 17:12:20 +00:00
Neil Horner
01e8652317
Use all point for volcano and tables [CW-7277]
2026-05-26 17:12:20 +00:00
Neil Horner
fa884c71c1
Clustering plots low data [CW-7275]
2026-05-26 17:10:46 +00:00
Sam Nicholls
175e6c9437
Per-sample pileup counts [CW-7196]
2026-05-26 09:52:38 +00:00
Neil Horner
020d555219
Add the missing annotation ref summary [CW-7271]
2026-05-22 17:05:56 +00:00
Kiah McIntosh
1f456da61d
SQANTI3 results in report [CW-7238]
2026-05-22 15:28:21 +00:00
Neil Horner
5823f04809
[CW-7211] Hierarchical plot + PCA
2026-05-22 14:34:50 +00:00
Natalia Garcia
2cfc7b2549
Use new sample sheet validation
2026-05-22 12:58:17 +00:00
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
