kfukuta/wf-transcriptomes-v202
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Author SHA1 Message Date
Chris Wright
63d9d14f17
Fix DE validation gating and per-sample NDR 2026-05-05 18:42:18 +01:00
Chris Wright
0633a6304d Merge branch 'r-test-infra-only' into 'dev' 
[CW-7161] Add workflow-local R test infrastructure

See merge request epi2melabs/workflows/wf-transcriptomes!236
 2026-05-05 17:10:10 +00:00
Chris Wright
f180b9e331 [CW-7161] Add workflow-local R test infrastructure 2026-05-05 17:10:10 +00:00
Chris Wright
c17d98d6f9 Merge branch 'main-null-read-filter' into 'dev' 
Exclude ingress samples with no reads

See merge request epi2melabs/workflows/wf-transcriptomes!237
 2026-05-05 16:40:24 +00:00
Chris Wright
9dd5895482 Exclude ingress samples with no reads 2026-05-05 16:40:24 +00:00
Chris Wright
dcc8c04f54 Merge branch 'refresh' into 'dev' 
Refresh

See merge request epi2melabs/workflows/wf-transcriptomes!232
 2026-05-05 14:10:04 +00:00
Chris Wright
43cf5bf42a Refresh workflow to use bambu, sqanti, and dexseq 2026-05-05 14:10:04 +00:00
Kiah McIntosh
ea18f68c50 Merge branch 'update-common' into 'dev' 
Update common sha

See merge request epi2melabs/workflows/wf-transcriptomes!230
 2026-04-17 14:01:28 +00:00
Kiah McIntosh
057fc0e886 Update common sha 2026-04-17 14:01:28 +00:00
Chris Wright
f4cae35818 Merge branch 'cjw-codex-clean' into 'dev' 
Bring up to date

See merge request epi2melabs/workflows/wf-transcriptomes!229
 2026-04-17 12:29:58 +00:00
Chris Wright
abbd3537ec Bring up to date 2026-04-17 12:29:57 +00:00
Kiah McIntosh
c7bebf6428 Merge branch 'mr-feature' into 'dev' 
Automated changes

See merge request epi2melabs/workflows/wf-transcriptomes!226
 2025-12-08 14:50:51 +00:00
Chris Wright
4fad6b85a8 Automated changes 2025-12-08 14:50:51 +00:00
Kiah McIntosh
924119c98f Merge branch 'tu-5.6.3' into 'dev' 
Template update v5.6.3 [CW-6859]

See merge request epi2melabs/workflows/wf-transcriptomes!227
 2025-12-05 18:16:59 +00:00
Kiah McIntosh
90e6453a8f Template update v5.6.3 [CW-6859] 2025-12-05 18:16:58 +00:00
Neil Horner
27d12e35ae Merge branch 'sgriffiths-dev-patch-45208' into 'dev' 
Update CHANGELOG.md

See merge request epi2melabs/workflows/wf-transcriptomes!224
 2025-10-17 10:02:29 +00:00
Sarah Griffiths
01387abb63 Update CHANGELOG.md 2025-10-17 09:57:39 +00:00
Neil Horner
27b57598ef Merge branch 'tag-1.7.2' into 'dev' 
tag v1.7.2

See merge request epi2melabs/workflows/wf-transcriptomes!223
 2025-10-17 08:43:45 +00:00
Sarah Griffiths
25b88c1321 tag v1.7.2 2025-10-17 08:43:44 +00:00
Rory Munro
297c87e92f Merge branch 'CW-6687/fix-workflow-title' into 'dev' 
Fix display title

See merge request epi2melabs/workflows/wf-transcriptomes!222
 2025-10-15 15:42:28 +00:00
Rory Munro
08ee6dc427
Fix display title 2025-10-14 17:23:38 +01:00
Sarah Griffiths
7d5abe0c55 Merge branch 'final-tag' into 'dev' 
tag v1.7.1

See merge request epi2melabs/workflows/wf-transcriptomes!220
 2025-08-01 15:02:39 +00:00
Sarah Griffiths
e83c92a0e5 tag v1.7.1 2025-08-01 15:02:39 +00:00
Neil Horner
e2a7d23009 Merge branch 'sample_col_check_CW-6532' into 'dev' 
Fix and simplify column name checking

Closes CW-6532

See merge request epi2melabs/workflows/wf-transcriptomes!221
 2025-08-01 09:14:20 +00:00
Neil Horner
4fe583d4ea Fix and simplify column name checking 2025-08-01 09:14:20 +00:00
Sarah Griffiths
7a94b2c515 Merge branch 'CW-6285' into 'dev' 
Output dexseq file [CW-6285]

Closes CW-6285

See merge request epi2melabs/workflows/wf-transcriptomes!219
 2025-07-29 08:54:20 +00:00
Sarah Griffiths
62e4266040 Output dexseq file [CW-6285] 2025-07-29 08:54:20 +00:00
Sarah Griffiths
a9e63518e5 Merge branch 'CW-6125' into 'dev' 
Filter out unstranded annotations and log warning [CW-6125]

Closes CW-6125

See merge request epi2melabs/workflows/wf-transcriptomes!218
 2025-06-20 08:43:15 +00:00
Sarah Griffiths
85b767358c Filter out unstranded annotations and log warning [CW-6125] 2025-06-20 08:43:15 +00:00
Neil Horner
9f18c3f0d5 Merge branch 'container_update_CW-5998' into 'dev' 
Container update CW-5998

See merge request epi2melabs/workflows/wf-transcriptomes!215
 2025-05-16 08:38:28 +00:00
Neil Horner
b2ac1edbb9 Container update CW-5998 2025-05-16 08:38:28 +00:00
Neil Horner
2df9061a48 Merge branch 'alias_hyphens_CW-5484' into 'dev' 
Fix hyphens in sample alias CW-5484

See merge request epi2melabs/workflows/wf-transcriptomes!212
 2025-05-14 13:55:02 +00:00
Neil Horner
19b54ba2ff Fix hyphens in sample alias CW-5484 2025-05-14 13:55:01 +00:00
Neil Horner
bb47d92ac2 Merge branch 'TU_5.6.1' into 'dev' 
Tu 5.6.1 [CW-6099]

See merge request epi2melabs/workflows/wf-transcriptomes!214
 2025-05-09 07:05:35 +00:00
Neil Horner
c84a197da5 Tu 5.6.1 [CW-6099] 2025-05-09 07:05:34 +00:00
Neil Horner
1b3f49a1ac Merge branch 'template_update_5.6.0' into 'dev' 
Template update 5.6.0 [CW-6070]

See merge request epi2melabs/workflows/wf-transcriptomes!213
 2025-05-06 10:23:01 +00:00
Neil Horner
18bf1d5b19 Template update 5.6.0 [CW-6070] 2025-05-06 10:23:01 +00:00
Sarah Griffiths
a74a34763e Merge branch 'memory_mac_ci' into 'dev' 
memory ci config

See merge request epi2melabs/workflows/wf-transcriptomes!211
 2025-04-15 11:20:42 +00:00
Sarah Griffiths
11c9221edc memory ci config 2025-04-15 11:20:42 +00:00
Sarah Griffiths
1d76e7326e Merge branch 'CW-5950' into 'dev' 
Fix aws/docker demo cmd [CW-5950]

Closes CW-5950

See merge request epi2melabs/workflows/wf-transcriptomes!210
 2025-04-11 13:22:49 +00:00
Sarah Griffiths
00c2e9a18b Fix aws/docker demo cmd [CW-5950] 2025-04-11 13:22:48 +00:00
Sarah Griffiths
cd97c1398e Merge branch 'CW-5911' into 'dev' 
Output BAMS in all cases apart from transcriptome-source precomputed [CW-5911]

Closes CW-5911

See merge request epi2melabs/workflows/wf-transcriptomes!209
 2025-04-03 12:57:58 +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
6f91cf59b1 Merge branch 'CW-5858' into 'dev' 
fix memory issue by replacing seq alignment stats with flagstat [CW-5858]

Closes CW-5858

See merge request epi2melabs/workflows/wf-transcriptomes!208
 2025-03-31 09:20:36 +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
60ec205339 Merge branch 'CW-5786' into 'dev' 
Only use exons in DE analysis [CW-5786]

Closes CW-5786

See merge request epi2melabs/workflows/wf-transcriptomes!207
 2025-03-28 09:58:05 +00:00
Sarah Griffiths
d5de051fd4 Only use exons in DE analysis [CW-5786] 2025-03-28 09:58:05 +00:00
Sarah Griffiths
9900143122 Merge branch 'CW-2965' into 'dev' 
Error message if ref_genome and ref_annotation mismatch CW-2965

Closes CW-2965

See merge request epi2melabs/workflows/wf-transcriptomes!202
 2025-03-14 19:06:47 +00:00
Sarah Griffiths
f9bd2ab574 Error message if ref_genome and ref_annotation mismatch CW-2965 2025-03-14 19:06:47 +00:00
Neil Horner
9ecd1345e9 Merge branch 'temp-update' into 'dev' 
Template v5.5.0 updates

See merge request epi2melabs/workflows/wf-transcriptomes!205
 2025-03-14 11:04:19 +00:00