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426 Commits

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Author SHA1 Message Date
Kiah McIntosh
eab8ef1efe Use args for R script inputs [CW-3398] 2025-02-07 08:42:49 +00:00
Neil Horner
91a514abd2 Merge branch 'schema_updates_CW-5529' into 'dev' 
Update schema

See merge request epi2melabs/workflows/wf-transcriptomes!197
 2025-01-23 10:59:32 +00:00
Neil Horner
e534921877 Update schema 2025-01-23 10:59:31 +00:00
Matt Parker
632a8f85a2 Merge branch 'split_bam_mem_CW-5352' into 'dev' 
Update memory for split_bam and  build_minimap_index_transcriptome

Closes CW-5352

See merge request epi2melabs/workflows/wf-transcriptomes!195
 2025-01-03 17:06:38 +00:00
Neil Horner
937a41f2cc Update memory for split_bam and build_minimap_index_transcriptome 2025-01-03 17:06:38 +00:00
Matt Parker
a33f3b967c Merge branch 'bump_v1.6.1' into 'dev' 
bump version

See merge request epi2melabs/workflows/wf-transcriptomes!196
 2025-01-03 12:44:09 +00:00
Neil Horner
39ef6ab16a bump version 2025-01-03 12:44:08 +00:00
Neil Horner
724a6515ea Merge branch 'empty_gff_CW-5438' into 'dev' 
Empty GFF bug CW-5438

See merge request epi2melabs/workflows/wf-transcriptomes!194
 2024-12-18 15:01:34 +00:00
Neil Horner
0ec44d03bd Empty GFF bug CW-5438 2024-12-18 15:01:33 +00:00
Matt Parker
74c19f1ea5 Merge branch 'bump_v1.6.0' into 'dev' 
Bump V1.6.0

See merge request epi2melabs/workflows/wf-transcriptomes!193
 2024-12-13 13:11:56 +00:00
Neil Horner
7ca3110648 Bump V1.6.0 2024-12-13 13:11:56 +00:00
Neil Horner
cb00ede5d8 Merge branch 'CW-5398' into 'dev' 
Access to undefined channel output bug CW-5398

Closes CW-5398

See merge request epi2melabs/workflows/wf-transcriptomes!192
 2024-12-13 11:51:07 +00:00
Neil Horner
c8c5922965 Access to undefined channel output bug CW-5398 2024-12-13 11:51:04 +00:00
Neil Horner
4c46f88f00 Merge branch 'gene_assignment_CW-5416' into 'dev' 
Account for stringtie multigene transcript artefacts

Closes CW-5369

See merge request epi2melabs/workflows/wf-transcriptomes!189
 2024-12-12 14:30:32 +00:00
Neil Horner
0a5c39cdf4 Account for stringtie multigene transcript artefacts 2024-12-12 14:30:31 +00:00
Neil Horner
112e87ad94 Merge branch 'template_2024_12_02' into 'dev' 
template update

See merge request epi2melabs/workflows/wf-transcriptomes!191
 2024-12-05 10:26:26 +00:00
Neil Horner
d38c7f3661 template update 2024-12-05 10:26:25 +00:00
Neil Horner
474c0fae3b Merge branch 'template_update_dec24' into 'dev' 
Update permissions

See merge request epi2melabs/workflows/wf-transcriptomes!190
 2024-12-02 12:55:51 +00:00
Neil Horner
624c16a3b1 Update permissions 2024-12-02 12:55:51 +00:00
Sarah Griffiths
b3fbb1117c Merge branch 'CW-3930' into 'dev' 
Actually output the dexseq file

Closes CW-3930

See merge request epi2melabs/workflows/wf-transcriptomes!188
 2024-11-05 11:51:40 +00:00
Sarah Griffiths
465d060933 Actually output the dexseq file 2024-11-05 11:51:40 +00:00
Neil Horner
45a717aaf3 Merge branch 'bokehreport_CW-3077' into 'dev' 
Update report CW-3077

See merge request epi2melabs/workflows/wf-transcriptomes!168
 2024-10-25 15:18:05 +00:00
Neil Horner
5c4780a1b2 Update report CW-3077 2024-10-25 15:18:05 +00:00
Sarah Griffiths
d2ddad27a2 Merge branch 'CW-4886' into 'dev' 
Tidy de analysis

Closes CW-4886

See merge request epi2melabs/workflows/wf-transcriptomes!185
 2024-09-16 09:26:13 +00:00
Sarah Griffiths
d83807f38d Tidy de analysis 2024-09-16 09:26:12 +00:00
Sam Nicholls
beb094ea85 Merge branch 'CW-4613-b' into 'dev' 
IGV absolute paths fix

Closes CW-4613

See merge request epi2melabs/workflows/wf-transcriptomes!184
 2024-09-13 11:48:16 +00:00
Sarah Griffiths
be1d322287 IGV absolute paths fix 2024-09-13 11:48:16 +00:00
Sarah Griffiths
ce4bfa9a30 Merge branch 'template-updates' into 'dev' 
Template updates

See merge request epi2melabs/workflows/wf-transcriptomes!183
 2024-09-11 12:47:01 +00:00
Sarah Griffiths
7ced52c05b Template updates 2024-09-11 12:47:01 +00:00
Sam Nicholls
31085d0fe4 Merge branch 'cw-4886' into 'dev' 
Output dtu_plots to local work dir then mv [CW-4886]

See merge request epi2melabs/workflows/wf-transcriptomes!182
 2024-09-09 18:41:18 +00:00
Sam Nicholls
46363987aa Output dtu_plots to local work dir then mv [CW-4886] 2024-09-09 18:41:17 +00:00
Sarah Griffiths
f8e08baed1 Merge branch 'CW-4613' into 'dev' 
CW-4613 IGV config

Closes CW-4613

See merge request epi2melabs/workflows/wf-transcriptomes!181
 2024-09-06 09:27:56 +00:00
Sarah Griffiths
14fe76dabc CW-4613 IGV config 2024-09-06 09:27:56 +00:00
Neil Horner
7287fdcdb1 Merge branch 'v1.3.0_fix' into 'dev' 
Missed v from version

See merge request epi2melabs/workflows/wf-transcriptomes!180
 2024-08-08 13:43:26 +00:00
Neil Horner
f62ec6c127 Missed v from version 2024-08-08 13:08:59 +01:00
Neil Horner
d7bb5c80f7 Merge branch 'pychopper_primer_CW_4184' into 'dev' 
Add new cDNA kits

See merge request epi2melabs/workflows/wf-transcriptomes!177
 2024-08-07 11:31:15 +00:00
Neil Horner
abc40d9015 Add new cDNA kits 2024-08-07 11:31:14 +00:00
Sam Nicholls
40456d676b Merge branch 'remove_jaffal_CW-4552' into 'dev' 
Remove fusion detection [CW-4552]

Closes CW-4552

See merge request epi2melabs/workflows/wf-transcriptomes!179
 2024-08-06 20:20:20 +00:00
Neil Horner
0200514536 Remove fusion detection [CW-4552] 2024-08-06 20:20:19 +00:00
Sam Nicholls
a037538744 Merge branch 'template_2024-07-10' into 'dev' 
template update 2024-07-10

See merge request epi2melabs/workflows/wf-transcriptomes!178
 2024-07-26 08:34:05 +00:00
Neil Horner
0f4eee002a template update 2024-07-10 2024-07-26 08:34:05 +00:00
Neil Horner
f01006c302 Merge branch 'v1.2.1' into 'dev' 
Bump v1.2.1

See merge request epi2melabs/workflows/wf-transcriptomes!176
 2024-07-04 14:48:31 +00:00
Neil Horner
a5699b2945 Bump v1.2.1 2024-07-04 14:48:30 +00:00
Neil Horner
3d5c4c38eb Merge branch 'template_update_0624' into 'dev' 
Template update

See merge request epi2melabs/workflows/wf-transcriptomes!175
 2024-07-04 13:25:20 +00:00
Neil Horner
c662293317 Template update 2024-06-27 16:13:55 +01:00
Neil Horner
1fed562746 Merge branch 'pychop_threads_CW-4010' into 'dev' 
Give pychopper more threads

See merge request epi2melabs/workflows/wf-transcriptomes!174
 2024-06-25 14:11:28 +00:00
Neil Horner
411290d5a4 Give pychopper more threads 2024-06-25 14:11:28 +00:00
Sarah Griffiths
d5df11cce4 Merge branch 'CW-3998' into 'dev' 
Handle annotations with no strand CW-3998

Closes CW-3998

See merge request epi2melabs/workflows/wf-transcriptomes!170
 2024-06-25 13:08:32 +00:00
Sarah Griffiths
57c0f5b303 Handle annotations with no strand CW-3998 2024-06-25 13:08:32 +00:00
Sam Nicholls
9353e23cc9 Merge branch 'bump_v1.2.0' into 'dev' 
Bump v1.2.0

See merge request epi2melabs/workflows/wf-transcriptomes!173
 2024-06-04 17:28:29 +00:00