Sam Nicholls
|
960ddbfc46
|
Stream collate RDS to reduce max mem [CW-7337]
|
2026-06-17 10:42:20 +00:00 |
|
Natalia Garcia
|
cd575b9fcb
|
IGV tracks mismatch index when there is one BAM per sample [CW-7332,CW-7349]
|
2026-06-16 14:25:43 +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
|
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 |
|
Harrison Pirt
|
d7a0e96a44
|
wf-transcriptomes 2.0.0-rc1
|
2026-05-28 10:54:49 +00:00 |
|
Chris Wright
|
43cf5bf42a
|
Refresh workflow to use bambu, sqanti, and dexseq
|
2026-05-05 14:10:04 +00:00 |
|
Kiah McIntosh
|
057fc0e886
|
Update common sha
|
2026-04-17 14:01:28 +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
|
01387abb63
|
Update CHANGELOG.md
|
2025-10-17 09:57:39 +00:00 |
|
Sarah Griffiths
|
25b88c1321
|
tag v1.7.2
|
2025-10-17 08:43:44 +00:00 |
|
Sarah Griffiths
|
e83c92a0e5
|
tag v1.7.1
|
2025-08-01 15:02:39 +00:00 |
|
Sarah Griffiths
|
62e4266040
|
Output dexseq file [CW-6285]
|
2025-07-29 08:54:20 +00:00 |
|
Sarah Griffiths
|
85b767358c
|
Filter out unstranded annotations and log warning [CW-6125]
|
2025-06-20 08:43:15 +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
|
c84a197da5
|
Tu 5.6.1 [CW-6099]
|
2025-05-09 07:05:34 +00:00 |
|
Neil Horner
|
18bf1d5b19
|
Template update 5.6.0 [CW-6070]
|
2025-05-06 10:23:01 +00:00 |
|
Sarah Griffiths
|
11c9221edc
|
memory ci config
|
2025-04-15 11:20:42 +00:00 |
|
Sarah Griffiths
|
00c2e9a18b
|
Fix aws/docker demo cmd [CW-5950]
|
2025-04-11 13:22:48 +00:00 |
|
Sarah Griffiths
|
390739cf8a
|
Output BAMS in all cases apart from transcriptome-source precomputed [CW-5911]
|
2025-04-03 12:57:58 +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
|
f9bd2ab574
|
Error message if ref_genome and ref_annotation mismatch CW-2965
|
2025-03-14 19:06:47 +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
|
e534921877
|
Update schema
|
2025-01-23 10:59:31 +00:00 |
|
Neil Horner
|
937a41f2cc
|
Update memory for split_bam and build_minimap_index_transcriptome
|
2025-01-03 17:06:38 +00:00 |
|
Neil Horner
|
39ef6ab16a
|
bump version
|
2025-01-03 12:44:08 +00:00 |
|
Neil Horner
|
0ec44d03bd
|
Empty GFF bug CW-5438
|
2024-12-18 15:01:33 +00:00 |
|
Neil Horner
|
7ca3110648
|
Bump V1.6.0
|
2024-12-13 13:11:56 +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 |
|
Sarah Griffiths
|
465d060933
|
Actually output the dexseq file
|
2024-11-05 11:51:40 +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 |
|
Sarah Griffiths
|
7ced52c05b
|
Template updates
|
2024-09-11 12:47:01 +00:00 |
|
Sarah Griffiths
|
14fe76dabc
|
CW-4613 IGV config
|
2024-09-06 09:27:56 +00:00 |
|
Neil Horner
|
f62ec6c127
|
Missed v from version
|
2024-08-08 13:08:59 +01:00 |
|
Neil Horner
|
abc40d9015
|
Add new cDNA kits
|
2024-08-07 11:31:14 +00:00 |
|
Neil Horner
|
0200514536
|
Remove fusion detection [CW-4552]
|
2024-08-06 20:20:19 +00:00 |
|
Neil Horner
|
a5699b2945
|
Bump v1.2.1
|
2024-07-04 14:48:30 +00:00 |
|
Neil Horner
|
1fed562746
|
Merge branch 'pychop_threads_CW-4010' into 'dev'
Give pychopper more threads
See merge request epi2melabs/workflows/wf-transcriptomes!174
|
2024-06-25 14:11:28 +00:00 |
|
Neil Horner
|
411290d5a4
|
Give pychopper more threads
|
2024-06-25 14:11:28 +00:00 |
|
Sarah Griffiths
|
57c0f5b303
|
Handle annotations with no strand CW-3998
|
2024-06-25 13:08:32 +00:00 |
|
Neil Horner
|
515c8c0ed8
|
Bump v1.2.0
|
2024-06-04 17:28:29 +00:00 |
|
Sarah Griffiths
|
63e0fe6524
|
change significance level to mark on MA plot
|
2024-04-10 08:09:23 +00:00 |
|