Sam Nicholls
c2656983d8
Merge branch 'exclude-data-artifacts' into 'dev'
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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'
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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'
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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'
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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'
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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'
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[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'
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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'
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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'
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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'
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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'
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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'
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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'
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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'
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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'
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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'
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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'
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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'
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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
4a3c1d1b35
Merge branch 'report_glow_up' into 'dev'
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[CW-7207] Volcanic
See merge request epi2melabs/workflows/wf-transcriptomes!249
2026-05-20 12:31:06 +00:00
Neil Horner
7194b38360
[CW-7207] Volcanic
2026-05-20 12:31:06 +00:00
Natalia Garcia
3e9d57a9e1
Merge branch 'tu-ruo-next-sample-sheet' into 'dev'
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Template updates (sample_sheet)
See merge request epi2melabs/workflows/wf-transcriptomes!278
2026-05-20 10:08:52 +00:00
Natalia Garcia
c3d38d9b34
Template updates (sample_sheet)
2026-05-20 10:08:52 +00:00
Natalia Garcia
c54ba7b0d7
Merge branch 'use-ruo-template' into 'dev'
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Pin wf-template@ruo-next
See merge request epi2melabs/workflows/wf-transcriptomes!276
2026-05-19 14:03:14 +00:00
Natalia Garcia
779388f871
Pin wf-template@ruo-next
2026-05-19 14:03:13 +00:00
Sam Nicholls
56ce8d2a7e
Merge branch 'em1e4' into 'dev'
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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
27f475d21a
Merge branch 'cw-7250' into 'dev'
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[CW-7250] fix up typography
See merge request epi2melabs/workflows/wf-transcriptomes!270
2026-05-18 15:14:53 +00:00
Chris Wright
68809a0147
[CW-7250] fix up typography
2026-05-18 15:14:53 +00:00
Chris Wright
0bd6f118b5
Merge branch 'cw-7210' into 'dev'
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[CW-7210] Add a sample sheet reader
See merge request epi2melabs/workflows/wf-transcriptomes!269
2026-05-18 14:14:20 +00:00
Chris Wright
980d08a29a
[CW-7210] Add a sample sheet reader
2026-05-18 14:14:19 +00:00
Kiah McIntosh
5d4009d92b
Merge branch 'cw-7246' into 'dev'
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Remove pychopper remnants [CW-7246]
See merge request epi2melabs/workflows/wf-transcriptomes!268
2026-05-18 12:54:01 +00:00
Kiah McIntosh
e35810dcea
Remove pychopper remnants [CW-7246]
2026-05-18 12:54:01 +00:00
