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Author SHA1 Message Date
Natalia Garcia
6ca2f2f027 Tidy up schema validation [CW-7278] 2026-05-26 18:42:11 +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
da5f78497e Merge branch 'hier_low_data_cw-7275' into 'dev' 
Clustering plots low data [CW-7275]

See merge request epi2melabs/workflows/wf-transcriptomes!298
 2026-05-26 17:10:46 +00:00
Neil Horner
fa884c71c1 Clustering plots low data [CW-7275] 2026-05-26 17:10:46 +00:00
Rory Munro
a4b08414cb Merge branch 'remove-bigwig' into 'dev' 
Remove bigwig CI test

See merge request epi2melabs/workflows/wf-transcriptomes!302
 2026-05-26 16:43:06 +00:00
Rory Munro
1192f09bc7 Remove bigwig CI test 2026-05-26 16:43:05 +00:00
Sarah Griffiths
c36404422e Merge branch 'CW-7274' into 'dev' 
Add force alignment option [CW-7274]

Closes CW-7274

See merge request epi2melabs/workflows/wf-transcriptomes!299
 2026-05-26 14:44:50 +00:00
Sarah Griffiths
3ca4511b5b Add force alignment option [CW-7274] 2026-05-26 14:44:50 +00:00
Rory Munro
6e72a4538c Merge branch 'rmunro-dev-patch-42566' into 'dev' 
Bump modkit sha version [CW-7273]

See merge request epi2melabs/workflows/wf-transcriptomes!297
 2026-05-26 12:31:05 +00:00
Rory Munro
86d100c869 Bump modkit sha version [CW-7273] 2026-05-26 12:31:05 +00:00
Kiah McIntosh
3d49d01ff2 Merge branch 'tube-map-update' into 'dev' 
Tube map update

See merge request epi2melabs/workflows/wf-transcriptomes!296
 2026-05-26 12:27:16 +00:00
Kiah McIntosh
dff1353790 Tube map update 2026-05-26 12:27:15 +00:00
Sam Nicholls
6327eda710 Merge branch 'cw-7196' into 'dev' 
Per-sample pileup counts [CW-7196]

See merge request epi2melabs/workflows/wf-transcriptomes!246
 2026-05-26 09:52:39 +00:00
Sam Nicholls
175e6c9437 Per-sample pileup counts [CW-7196] 2026-05-26 09:52:38 +00:00
Sam Nicholls
c2656983d8 Merge branch 'exclude-data-artifacts' into 'dev' 
CI : Exclude downloaded data artifacts

See merge request epi2melabs/workflows/wf-transcriptomes!293
 2026-05-26 08:04:59 +00:00
Sam Nicholls
6c0a59581f CI : Exclude downloaded data artifacts 2026-05-26 08:04:59 +00:00
Natalia Garcia
c87a5ce09c Merge branch 'CW-7212' into 'dev' 
Exclude non existent samples or samples without reads after ingress

Closes CW-7212

See merge request epi2melabs/workflows/wf-transcriptomes!255
 2026-05-26 07:53:34 +00:00
Natalia Garcia
04ddfbf872 Exclude non existent samples or samples without reads after ingress 2026-05-26 07:53:34 +00:00
Sarah Griffiths
d416441e11 Merge branch 'CW-7271_missing_summary' into 'dev' 
Add the missing annotation ref summary [CW-7271]

Closes CW-7271

See merge request epi2melabs/workflows/wf-transcriptomes!290
 2026-05-22 17:05:56 +00:00
Neil Horner
020d555219 Add the missing annotation ref summary [CW-7271] 2026-05-22 17:05:56 +00:00
Kiah McIntosh
a5c25ec0a1 Merge branch 'tube-map-modkit' into 'dev' 
Add modkit to tube map

See merge request epi2melabs/workflows/wf-transcriptomes!292
 2026-05-22 16:33:01 +00:00
Kiah McIntosh
df2d333797 Add modkit to tube map 2026-05-22 16:33:01 +00:00
Kiah McIntosh
50b971604e Merge branch 'cw-7238' into 'dev' 
SQANTI3 results in report [CW-7238]

See merge request epi2melabs/workflows/wf-transcriptomes!271
 2026-05-22 15:28:21 +00:00
Kiah McIntosh
1f456da61d SQANTI3 results in report [CW-7238] 2026-05-22 15:28:21 +00:00
Neil Horner
845c03f7f5 Merge branch 'hier_plots' into 'dev' 
[CW-7211] Hierarchical plot + PCA

See merge request epi2melabs/workflows/wf-transcriptomes!251
 2026-05-22 14:34:50 +00:00
Neil Horner
5823f04809 [CW-7211] Hierarchical plot + PCA 2026-05-22 14:34:50 +00:00
Natalia Garcia
3204d24045 Merge branch 'template-updates' into 'dev' 
Use new sample sheet validation

See merge request epi2melabs/workflows/wf-transcriptomes!289
 2026-05-22 12:58:17 +00:00
Natalia Garcia
2cfc7b2549 Use new sample sheet validation 2026-05-22 12:58:17 +00:00
Neil Horner
1b3155d591 Merge branch 'report_glow_up_2' into 'dev' 
Report glow up 2 [CW-7207]

See merge request epi2melabs/workflows/wf-transcriptomes!279
 2026-05-22 11:55:44 +00:00
Neil Horner
f45056c438 Report glow up 2 [CW-7207] 2026-05-22 11:55:44 +00:00
Kiah McIntosh
8c6196ddc1 Merge branch 'cw-7270-readme' into 'dev' 
Update readme for alignment and ingress outputs [CW-7270]

See merge request epi2melabs/workflows/wf-transcriptomes!288
 2026-05-22 10:44:40 +00:00
Kiah McIntosh
90cc4cf73b Update readme for alignment and ingress outputs [CW-7270] 2026-05-22 10:44:40 +00:00
Sam Nicholls
89626ab016 Merge branch 'gene_names' into 'dev' 
Add gene name to TSV outputs [CW-7160]

See merge request epi2melabs/workflows/wf-transcriptomes!274
 2026-05-22 10:23:21 +00:00
Neil Horner
d9c9cc6765 Add gene name to TSV outputs [CW-7160] 2026-05-22 10:23:21 +00:00
Rory Munro
a86d325393 Merge branch 'override-singularity' into 'dev' 
Override singularity CI

See merge request epi2melabs/workflows/wf-transcriptomes!287
 2026-05-22 10:15:55 +00:00
Rory Munro
bfebfaa4b3 Override singularity CI 2026-05-22 10:15:55 +00:00
Sarah Griffiths
dac0a6ef01 Merge branch 'CW-7261-b' into 'dev' 
Annotation quant issues test [CW-7261]

Closes CW-7261

See merge request epi2melabs/workflows/wf-transcriptomes!284
 2026-05-22 09:38:34 +00:00
Sarah Griffiths
7b94eb2ca0 Annotation quant issues test [CW-7261] 2026-05-22 09:38:33 +00:00
Kiah McIntosh
176762fbe7 Merge branch 'alignment-outputs' into 'dev' 
Alignment outputs in per sample folder [CW-7270]

See merge request epi2melabs/workflows/wf-transcriptomes!280
 2026-05-22 09:12:26 +00:00
Kiah McIntosh
f5e5f3a790 Alignment outputs in per sample folder [CW-7270] 2026-05-22 09:12:26 +00:00
Kiah McIntosh
18e0c5e92f Merge branch 'cw-7208' into 'dev' 
Skip cohort processes when n=1 [CW-7208]

See merge request epi2melabs/workflows/wf-transcriptomes!267
 2026-05-21 16:19:18 +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
Kiah McIntosh
e98a3f14be Merge branch 'cw-7264' into 'dev' 
Sort joint bambu inputs to fix caching [CW-7264]

See merge request epi2melabs/workflows/wf-transcriptomes!282
 2026-05-20 16:31:25 +00:00
Kiah McIntosh
d124d8ba73 Sort joint bambu inputs to fix caching [CW-7264] 2026-05-20 16:31:24 +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