Neil Horner
725768cebb
Enforce str dtype for sample metadata [CW-7394]
2026-07-14 11:48:48 +00:00
Sam Nicholls
4613584c69
Improve messaging for seqnames with no transcript records [CW-7391]
2026-07-13 16:00:41 +00:00
Neil Horner
58b8582ea5
Volcano ylim slider [CW-7354]
2026-06-18 08:34:14 +00:00
Neil Horner
2ed160cbe7
Volcano filter NA [CW-7345]
2026-06-16 13:02:23 +00:00
Neil Horner
c99ba8cd9f
Sci format for volcano padj values [CW-7342]
2026-06-16 10:17:59 +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
Kiah McIntosh
759cb9d868
Skip cohort processes when n=1 [CW-7208]
2026-05-21 16:19:18 +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
Chris Wright
68809a0147
[CW-7250] fix up typography
2026-05-18 15:14:53 +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
3d7d49795e
[CW-7235] cast ? to . in gffs
2026-05-16 13:22:47 +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
3e0dfd21e2
[CW-7166] [CW-7169] Reference and annotation preparation
2026-05-07 10:09:36 +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
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
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
b62722751f
Fix overwritten DGE results file
2025-02-18 17:05:45 +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
7ced52c05b
Template updates
2024-09-11 12:47:01 +00:00
