kfukuta/wf-transcriptomes-v202
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4613584c69
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Author SHA1 Message Date
Sam Nicholls
4613584c69 Improve messaging for seqnames with no transcript records [CW-7391] 2026-07-13 16:00:41 +00:00
Sarah Griffiths
c09fa66ffc Merge branch 'CW-7387' into 'dev' 
Remove analysis_group mention [CW-7387]

Closes CW-7387

See merge request epi2melabs/workflows/wf-transcriptomes!343
 2026-07-10 09:54:05 +00:00
Sarah Griffiths
66655043ea Remove analysis_group mention [CW-7387] 2026-07-10 09:54:04 +00:00
Neil Horner
d3d2a15efd Merge branch 'uf_wrong_CW-7384' into 'dev' 
Use -ub for cDNA [CW-7384]

Closes CW-7384

See merge request epi2melabs/workflows/wf-transcriptomes!341
 2026-07-08 11:41:38 +00:00
Neil Horner
8f863575c0 Use -ub for cDNA [CW-7384] 2026-07-08 11:41:37 +00:00
Sam Nicholls
3040c2796c Merge branch 'v201-changelog' into 'dev' 
wf-transcriptomics 2.0.1

See merge request epi2melabs/workflows/wf-transcriptomes!340
 2026-06-18 09:12:55 +00:00
Sam Nicholls
bac1638b49 wf-transcriptomics 2.0.1 2026-06-18 09:12:55 +00:00
Neil Horner
50fd84597d Merge branch 'yaxisrange_CW-7354' into 'dev' 
Volcano ylim slider [CW-7354]

See merge request epi2melabs/workflows/wf-transcriptomes!339
 2026-06-18 08:34:14 +00:00
Neil Horner
58b8582ea5 Volcano ylim slider [CW-7354] 2026-06-18 08:34:14 +00:00
Sam Nicholls
cca505faae Merge branch 'cw-7337' into 'dev' 
Stream collate RDS to reduce max mem [CW-7337]

See merge request epi2melabs/workflows/wf-transcriptomes!338
 2026-06-17 10:42:21 +00:00
Sam Nicholls
960ddbfc46 Stream collate RDS to reduce max mem [CW-7337] 2026-06-17 10:42:20 +00:00
Natalia Garcia
f698102333 Merge branch 'CW-7332' into 'dev' 
IGV tracks mismatch index when there is one BAM per sample [CW-7332,CW-7349]

Closes CW-7332

See merge request epi2melabs/workflows/wf-transcriptomes!332
 2026-06-16 14:25:44 +00:00
Natalia Garcia
cd575b9fcb IGV tracks mismatch index when there is one BAM per sample [CW-7332,CW-7349] 2026-06-16 14:25:43 +00:00
Neil Horner
13ce17c631 Merge branch 'na_volcano_CW-7345' into 'dev' 
Volcano filter NA [CW-7345]

See merge request epi2melabs/workflows/wf-transcriptomes!335
 2026-06-16 13:02:23 +00:00
Neil Horner
2ed160cbe7 Volcano filter NA [CW-7345] 2026-06-16 13:02:23 +00:00
Neil Horner
a30eaf2ffc Merge branch 'scinot_CW-7342' into 'dev' 
Sci format for volcano padj values [CW-7342]

See merge request epi2melabs/workflows/wf-transcriptomes!336
 2026-06-16 10:17:59 +00:00
Neil Horner
c99ba8cd9f Sci format for volcano padj values [CW-7342] 2026-06-16 10:17:59 +00:00
Sam Nicholls
0aa3ce3cad Merge branch 'cw-7338' into 'dev' 
Chunk RDS from disk if provided a path [CW-7338]

See merge request epi2melabs/workflows/wf-transcriptomes!334
 2026-06-15 13:38:03 +00:00
Sam Nicholls
760ffa009e Chunk RDS from disk if provided a path [CW-7338] 2026-06-15 13:38:02 +00:00
Sam Nicholls
3d04f3485a Merge branch 'cw-7333' into 'dev' 
Handle full join fail during bambu quant [CW-7333]

See merge request epi2melabs/workflows/wf-transcriptomes!333
 2026-06-12 16:03:48 +00:00
Sam Nicholls
6099173238 Handle full join fail during bambu quant [CW-7333] 2026-06-12 16:03:48 +00:00
Sam Nicholls
94823e73d1 Use xlarge-highio 2026-06-09 12:08:19 +00:00
Sam Nicholls
fbb1529816 Use smoke_de as default CI test 2026-06-09 12:04:53 +00:00
Sam Nicholls
1fa032ae0e Merge branch 'v200-rc2' into 'dev' 
wf-transcriptomes v2.0.0

See merge request epi2melabs/workflows/wf-transcriptomes!320
 2026-06-09 11:58:17 +00:00
Sam Nicholls
c21588761b wf-transcriptomes v2.0.0 2026-06-09 11:58:17 +00:00
Sam Nicholls
f1dbc69191 Merge branch 'v2releasechanglog' into 'dev' 
wf-transcriptomes 2.0.0-rc1

See merge request epi2melabs/workflows/wf-transcriptomes!315
 2026-05-28 10:54:50 +00:00
Harrison Pirt
d7a0e96a44 wf-transcriptomes 2.0.0-rc1 2026-05-28 10:54:49 +00:00
Neil Horner
0b7dbdb294 Merge branch 'devon-docs' into 'dev' 
Final README pass

See merge request epi2melabs/workflows/wf-transcriptomes!317
 2026-05-28 10:21:37 +00:00
Chris Wright
957e57d87b Final README pass 2026-05-28 10:21:37 +00:00
Sam Nicholls
274548f64f Merge branch 'remove_demo' into 'dev' 
Remove demo data to avoid breaking production demo

See merge request epi2melabs/workflows/wf-transcriptomes!318
 2026-05-28 07:15:20 +00:00
Sarah Griffiths
30a9880bf7 Remove demo data to avoid breaking production demo 2026-05-28 07:15:20 +00:00
Sarah Griffiths
334173d613 Merge branch 'report-explain' into 'dev' 
Add brief description to each section in report

See merge request epi2melabs/workflows/wf-transcriptomes!314
 2026-05-27 16:17:22 +00:00
Sarah Griffiths
e17fec8bc0 Add brief description to each section in report 2026-05-27 16:17:22 +00:00
Sarah Griffiths
0129592acc Merge branch 'tidy-params' into 'dev' 
Tidy params

See merge request epi2melabs/workflows/wf-transcriptomes!283
 2026-05-27 15:40:53 +00:00
Sam Nicholls
bca0f01bf6 Tidy params 2026-05-27 15:40:53 +00:00
Neil Horner
26d830a916 Merge branch 'condition_report_fix' into 'dev' 
Condition report fix [CW-7283]

See merge request epi2melabs/workflows/wf-transcriptomes!313
 2026-05-27 15:05:18 +00:00
Neil Horner
3e53b755cc Condition report fix [CW-7283] 2026-05-27 15:05:18 +00:00
Sarah Griffiths
541de0c1f9 Merge branch 'stop-demo-release' into 'dev' 
Avoid publishing demo for transcriptomes

See merge request epi2melabs/workflows/wf-transcriptomes!316
 2026-05-27 14:37:54 +00:00
Sarah Griffiths
ef08219e11 Avoid publishing demo for transcriptomes 2026-05-27 14:37:53 +00:00
Neil Horner
10b2013b6a Merge branch 'transcriptome_table_order' into 'dev' 
Report minor fixes [CW-7281]

See merge request epi2melabs/workflows/wf-transcriptomes!309
 2026-05-27 13:20:41 +00:00
Neil Horner
722d736f24 Report minor fixes [CW-7281] 2026-05-27 13:20:41 +00:00
Sam Nicholls
9cba80832d Merge branch 'unnecessary-igv' into 'dev' 
Publish refs for IGV only when necessary [CW-7280]

See merge request epi2melabs/workflows/wf-transcriptomes!306
 2026-05-27 12:24:08 +00:00
Sam Nicholls
262f49944e Publish refs for IGV only when necessary [CW-7280] 2026-05-27 12:24:07 +00:00
Natalia Garcia
c96be955b5 Merge branch 'template-updates-sorting' into 'dev' 
Template updates: sort threads param

See merge request epi2melabs/workflows/wf-transcriptomes!311
 2026-05-27 11:59:12 +00:00
Natalia Garcia
531975c004 Template updates: sort threads param 2026-05-27 11:59:11 +00:00
Natalia Garcia
d73b9a2721 Merge branch 'template-updates2' into 'dev' 
Template updates: reference

See merge request epi2melabs/workflows/wf-transcriptomes!310
 2026-05-27 10:00:41 +00:00
Natalia Garcia
9d59c6b902 Template updates: reference 2026-05-27 10:00:40 +00:00
Natalia Garcia
33ad57cdaa Merge branch 'CW-7279' into 'dev' 
Use mode copy in publishDir [CW-7279]

Closes CW-7279

See merge request epi2melabs/workflows/wf-transcriptomes!308
 2026-05-27 09:29:30 +00:00
Natalia Garcia
7e301319fc Use mode copy in publishDir [CW-7279] 2026-05-27 09:29:30 +00:00
Sam Nicholls
dda764f48c Merge branch 'cw-7196-b' into 'dev' 
Per-sample mod summary

See merge request epi2melabs/workflows/wf-transcriptomes!294
 2026-05-27 08:11:02 +00:00