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
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
Sam Nicholls
a011a2dc1f
Merge branch 'chunk-quant' into 'dev'
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Scatter-gather bambu quant [CW-7201]
See merge request epi2melabs/workflows/wf-transcriptomes!256
2026-05-18 12:29:48 +00:00
Sam Nicholls
db744dbe81
Scatter-gather bambu quant [CW-7201]
2026-05-18 12:29:48 +00:00
Chris Wright
e9b68d6222
Merge branch 'cw-7221' into 'dev'
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[CW-7221] Fix various pathological cases
See merge request epi2melabs/workflows/wf-transcriptomes!266
2026-05-18 10:58:19 +00:00
Chris Wright
8f093ed675
[CW-7221] Fix various pathological cases
2026-05-18 10:58:18 +00:00
Natalia Garcia
8aa0228b21
Merge branch 'CW-7234-igv' into 'dev'
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Restore IGV [CW-7234]
Closes CW-7234
See merge request epi2melabs/workflows/wf-transcriptomes!260
2026-05-18 09:41:50 +00:00
Natalia Garcia
4dfd5f06e7
Restore IGV [CW-7234]
2026-05-18 09:41:49 +00:00
Chris Wright
2d0ff5da08
Merge branch 'trivial' into 'dev'
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Return the correct annotation
See merge request epi2melabs/workflows/wf-transcriptomes!264
2026-05-18 09:31:53 +00:00
Chris Wright
fc72470071
Merge branch 'CW-7472' into 'dev'
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[CW-7472] Fix a formatting issue
Closes CW-7472
See merge request epi2melabs/workflows/wf-transcriptomes!265
2026-05-17 11:00:25 +00:00
Chris Wright
aa85daafcf
[CW-7472] Fix a formatting issue
2026-05-17 11:00:25 +00:00
Chris Wright
c21c609017
Return the correct annotation
2026-05-16 17:02:03 +01:00
Chris Wright
e2166fe062
Merge branch 'cw-7235' into 'dev'
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[CW-7235] cast ? to . in gffs
See merge request epi2melabs/workflows/wf-transcriptomes!261
2026-05-16 13:22:47 +00:00
Chris Wright
3d7d49795e
[CW-7235] cast ? to . in gffs
2026-05-16 13:22:47 +00:00
Chris Wright
41c5f55e2f
Merge branch 'cw-7192' into 'dev'
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[CW-7192] remove full length filtering
See merge request epi2melabs/workflows/wf-transcriptomes!262
2026-05-15 15:15:07 +00:00
Chris Wright
31d1ffe038
[CW-7192] remove full length filtering
2026-05-15 15:15:07 +00:00
Chris Wright
855fbb69b2
Merge branch 'cw-7241' into 'dev'
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[CW-7241] Fix potential issue resulting from transcript filtering
See merge request epi2melabs/workflows/wf-transcriptomes!259
2026-05-14 21:48:37 +00:00
Chris Wright
b2be586505
[CW-7241] Fix potential issue resulting from transcript filtering
2026-05-14 21:48:37 +00:00
Chris Wright
7278f98831
Merge branch 'ci-matrix' into 'dev'
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[CW-7231] clean up ci test matrix
See merge request epi2melabs/workflows/wf-transcriptomes!258
2026-05-14 21:40:49 +00:00
Chris Wright
d4c9101e27
[CW-7231] clean up ci test matrix
2026-05-14 21:40:48 +00:00
Chris Wright
d38b7bf271
Merge branch 'arrrrrrgs' into 'dev'
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[CW-7214] Tidy up CLI parsing
See merge request epi2melabs/workflows/wf-transcriptomes!252
2026-05-14 17:41:21 +00:00
Chris Wright
5af948dabf
[CW-7214] Tidy up CLI parsing
2026-05-14 17:41:21 +00:00
Sam Nicholls
a08e23849d
Merge branch 'unbreak-multisample' into 'dev'
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Use value channels for refs crossing samples
See merge request epi2melabs/workflows/wf-transcriptomes!257
2026-05-14 17:18:57 +00:00
Sam Nicholls
678f1de3f1
Use value channels for refs crossing samples
2026-05-14 17:18:57 +00:00
Neil Horner
b87c916247
Merge branch 'logfold_column_CW-7233' into 'dev'
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Rename log2Fold_contrast column [CW-7233]
See merge request epi2melabs/workflows/wf-transcriptomes!253
2026-05-14 14:53:08 +00:00
Neil Horner
1fb62d41df
Rename log2Fold_contrast column [CW-7233]
2026-05-14 14:53:08 +00:00
Kiah McIntosh
4fa78ea462
Merge branch 'tubemap' into 'dev'
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Add tube map [CW-7218]
See merge request epi2melabs/workflows/wf-transcriptomes!254
2026-05-14 10:50:19 +00:00
Kiah McIntosh
225f9c4a44
Add tube map [CW-7218]
2026-05-14 10:50:18 +00:00
Sam Nicholls
42d29d3a4d
Merge branch 'template-ingress' into 'dev'
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Use new alignment ingress [CW-7186][CW-7202][CW-7229]
See merge request epi2melabs/workflows/wf-transcriptomes!247
2026-05-14 09:12:38 +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'
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[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
Sam Nicholls
4e65dba188
Merge branch 'cw-7185' into 'dev'
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Increase prepareAnnotationReference memory [CW-7185]
See merge request epi2melabs/workflows/wf-transcriptomes!244
2026-05-08 21:04:12 +00:00
Kiah McIntosh
c783fdf6c6
Increase prepareAnnotationReference memory [CW-7185]
2026-05-08 21:04:12 +00:00
Natalia Garcia
0eb808b605
Merge branch 'CW-7191' into 'dev'
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Add missing directives [CW-7191]
Closes CW-7191
See merge request epi2melabs/workflows/wf-transcriptomes!240
2026-05-08 14:56:31 +00:00
Natalia Garcia
d7337638f8
Add missing directives [CW-7191]
2026-05-08 14:56:31 +00:00
