Chris Wright
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e9b68d6222
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Merge branch 'cw-7221' into 'dev'
[CW-7221] Fix various pathological cases
See merge request epi2melabs/workflows/wf-transcriptomes!266
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2026-05-18 10:58:19 +00:00 |
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Chris Wright
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8f093ed675
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[CW-7221] Fix various pathological cases
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2026-05-18 10:58:18 +00:00 |
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Natalia Garcia
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8aa0228b21
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Merge branch 'CW-7234-igv' into 'dev'
Restore IGV [CW-7234]
Closes CW-7234
See merge request epi2melabs/workflows/wf-transcriptomes!260
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2026-05-18 09:41:50 +00:00 |
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Natalia Garcia
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4dfd5f06e7
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Restore IGV [CW-7234]
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2026-05-18 09:41:49 +00:00 |
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Chris Wright
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2d0ff5da08
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Merge branch 'trivial' into 'dev'
Return the correct annotation
See merge request epi2melabs/workflows/wf-transcriptomes!264
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2026-05-18 09:31:53 +00:00 |
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Chris Wright
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fc72470071
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Merge branch 'CW-7472' into 'dev'
[CW-7472] Fix a formatting issue
Closes CW-7472
See merge request epi2melabs/workflows/wf-transcriptomes!265
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2026-05-17 11:00:25 +00:00 |
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Chris Wright
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aa85daafcf
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[CW-7472] Fix a formatting issue
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2026-05-17 11:00:25 +00:00 |
|
Chris Wright
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c21c609017
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Return the correct annotation
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2026-05-16 17:02:03 +01:00 |
|
Chris Wright
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e2166fe062
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Merge branch 'cw-7235' into 'dev'
[CW-7235] cast ? to . in gffs
See merge request epi2melabs/workflows/wf-transcriptomes!261
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2026-05-16 13:22:47 +00:00 |
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Chris Wright
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3d7d49795e
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[CW-7235] cast ? to . in gffs
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2026-05-16 13:22:47 +00:00 |
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Chris Wright
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41c5f55e2f
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Merge branch 'cw-7192' into 'dev'
[CW-7192] remove full length filtering
See merge request epi2melabs/workflows/wf-transcriptomes!262
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2026-05-15 15:15:07 +00:00 |
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Chris Wright
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31d1ffe038
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[CW-7192] remove full length filtering
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2026-05-15 15:15:07 +00:00 |
|
Chris Wright
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855fbb69b2
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Merge branch 'cw-7241' into 'dev'
[CW-7241] Fix potential issue resulting from transcript filtering
See merge request epi2melabs/workflows/wf-transcriptomes!259
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2026-05-14 21:48:37 +00:00 |
|
Chris Wright
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b2be586505
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[CW-7241] Fix potential issue resulting from transcript filtering
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2026-05-14 21:48:37 +00:00 |
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Chris Wright
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7278f98831
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Merge branch 'ci-matrix' into 'dev'
[CW-7231] clean up ci test matrix
See merge request epi2melabs/workflows/wf-transcriptomes!258
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2026-05-14 21:40:49 +00:00 |
|
Chris Wright
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d4c9101e27
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[CW-7231] clean up ci test matrix
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2026-05-14 21:40:48 +00:00 |
|
Chris Wright
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d38b7bf271
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Merge branch 'arrrrrrgs' into 'dev'
[CW-7214] Tidy up CLI parsing
See merge request epi2melabs/workflows/wf-transcriptomes!252
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2026-05-14 17:41:21 +00:00 |
|
Chris Wright
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5af948dabf
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[CW-7214] Tidy up CLI parsing
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2026-05-14 17:41:21 +00:00 |
|
Sam Nicholls
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a08e23849d
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Merge branch 'unbreak-multisample' into 'dev'
Use value channels for refs crossing samples
See merge request epi2melabs/workflows/wf-transcriptomes!257
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2026-05-14 17:18:57 +00:00 |
|
Sam Nicholls
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678f1de3f1
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Use value channels for refs crossing samples
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2026-05-14 17:18:57 +00:00 |
|
Neil Horner
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b87c916247
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Merge branch 'logfold_column_CW-7233' into 'dev'
Rename log2Fold_contrast column [CW-7233]
See merge request epi2melabs/workflows/wf-transcriptomes!253
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2026-05-14 14:53:08 +00:00 |
|
Neil Horner
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1fb62d41df
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Rename log2Fold_contrast column [CW-7233]
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2026-05-14 14:53:08 +00:00 |
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Kiah McIntosh
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4fa78ea462
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Merge branch 'tubemap' into 'dev'
Add tube map [CW-7218]
See merge request epi2melabs/workflows/wf-transcriptomes!254
|
2026-05-14 10:50:19 +00:00 |
|
Kiah McIntosh
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225f9c4a44
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Add tube map [CW-7218]
|
2026-05-14 10:50:18 +00:00 |
|
Sam Nicholls
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42d29d3a4d
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Merge branch 'template-ingress' into 'dev'
Use new alignment ingress [CW-7186][CW-7202][CW-7229]
See merge request epi2melabs/workflows/wf-transcriptomes!247
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2026-05-14 09:12:38 +00:00 |
|
Sam Nicholls
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06d77b2543
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Use new alignment ingress [CW-7186][CW-7202][CW-7229]
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2026-05-14 09:12:38 +00:00 |
|
Chris Wright
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a99e5cda04
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Merge branch 'cw-7172' into 'dev'
[CW-7172] Improve testing and reporting on differential analysis analysis
See merge request epi2melabs/workflows/wf-transcriptomes!242
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2026-05-11 09:42:54 +00:00 |
|
Chris Wright
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f2458c5603
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[CW-7172] Improve testing and reporting on differential analysis analysis
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2026-05-11 09:42:54 +00:00 |
|
Sam Nicholls
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4e65dba188
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Merge branch 'cw-7185' into 'dev'
Increase prepareAnnotationReference memory [CW-7185]
See merge request epi2melabs/workflows/wf-transcriptomes!244
|
2026-05-08 21:04:12 +00:00 |
|
Kiah McIntosh
|
c783fdf6c6
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Increase prepareAnnotationReference memory [CW-7185]
|
2026-05-08 21:04:12 +00:00 |
|
Natalia Garcia
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0eb808b605
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Merge branch 'CW-7191' into 'dev'
Add missing directives [CW-7191]
Closes CW-7191
See merge request epi2melabs/workflows/wf-transcriptomes!240
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2026-05-08 14:56:31 +00:00 |
|
Natalia Garcia
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d7337638f8
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Add missing directives [CW-7191]
|
2026-05-08 14:56:31 +00:00 |
|
Sam Nicholls
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909065a298
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Merge branch 'no_bioc_online_check_cw7194' into 'dev'
No bioc version check [CW-7194]
See merge request epi2melabs/workflows/wf-transcriptomes!243
|
2026-05-08 14:08:37 +00:00 |
|
Neil Horner
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543b39bd79
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No bioc version check [CW-7194]
|
2026-05-08 14:08:37 +00:00 |
|
Chris Wright
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247f1aaf0b
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Merge branch 'r-tests' into 'dev'
[CW-7161] R tests
See merge request epi2melabs/workflows/wf-transcriptomes!235
|
2026-05-08 07:55:06 +00:00 |
|
Chris Wright
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508a6b0525
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[CW-7161] R tests
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2026-05-08 07:55:06 +00:00 |
|
Kiah McIntosh
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9ddec6ff61
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Merge branch 'ref-prep' into 'dev'
[CW-7166] [CW-7169] Reference and annotation preparation
See merge request epi2melabs/workflows/wf-transcriptomes!239
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2026-05-07 10:09:36 +00:00 |
|
Chris Wright
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3e0dfd21e2
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[CW-7166] [CW-7169] Reference and annotation preparation
|
2026-05-07 10:09:36 +00:00 |
|
Chris Wright
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265b462cc6
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Merge branch 'de-validation-ndr-fixes' into 'dev'
Fix DE validation gating and per-sample NDR
See merge request epi2melabs/workflows/wf-transcriptomes!238
|
2026-05-06 08:16:28 +00:00 |
|
Chris Wright
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63d9d14f17
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Fix DE validation gating and per-sample NDR
|
2026-05-05 18:42:18 +01:00 |
|
Chris Wright
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0633a6304d
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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
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[CW-7161] Add workflow-local R test infrastructure
|
2026-05-05 17:10:10 +00:00 |
|
Chris Wright
|
c17d98d6f9
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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
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Merge branch 'refresh' into 'dev'
Refresh
See merge request epi2melabs/workflows/wf-transcriptomes!232
|
2026-05-05 14:10:04 +00:00 |
|
Chris Wright
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43cf5bf42a
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Refresh workflow to use bambu, sqanti, and dexseq
|
2026-05-05 14:10:04 +00:00 |
|
Kiah McIntosh
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ea18f68c50
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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
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057fc0e886
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Update common sha
|
2026-04-17 14:01:28 +00:00 |
|
Chris Wright
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f4cae35818
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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 |
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Chris Wright
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abbd3537ec
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Bring up to date
|
2026-04-17 12:29:57 +00:00 |
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