kfukuta/wf-transcriptomes-v202
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451 Commits

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Author SHA1 Message Date
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
Neil Horner
515c8c0ed8 Bump v1.2.0 2024-06-04 17:28:29 +00:00
Neil Horner
f89a61d304 Merge branch 'bams_CW-3512' into 'dev' 
BAM input CW-3512

See merge request epi2melabs/workflows/wf-transcriptomes!172
 2024-06-04 09:25:35 +00:00
Neil Horner
cfa41f16d0 BAM input CW-3512 2024-06-04 09:25:31 +00:00
Natalia Garcia
7ca0d269f4 Merge branch 'template_2024-05-24' into 'dev' 
Template update 2024 05 24

See merge request epi2melabs/workflows/wf-transcriptomes!171
 2024-05-30 19:40:11 +00:00
Neil Horner
e2585dcd11 Template update 2024 05 24 2024-05-30 19:40:11 +00:00
Sam Nicholls
39cc58ae9e Merge branch 'temp-update' into 'dev' 
Temp update

See merge request epi2melabs/workflows/wf-transcriptomes!167
 2024-05-10 08:42:13 +00:00
Sarah Griffiths
d7fcb2d5f7 Temp update 2024-05-10 08:42:12 +00:00
Sarah Griffiths
6f2ac3241b Merge branch 'CW-3244' into 'dev' 
change significance level to mark on MA plot

Closes CW-3244

See merge request epi2melabs/workflows/wf-transcriptomes!164
 2024-04-10 08:09:23 +00:00
Sarah Griffiths
63e0fe6524 change significance level to mark on MA plot 2024-04-10 08:09:23 +00:00
Sarah Griffiths
f85e039f98 Merge branch 'template-update' into 'dev' 
Template update

See merge request epi2melabs/workflows/wf-transcriptomes!166
 2024-04-03 09:47:30 +00:00
Sarah Griffiths
595aae4006 Template update 2024-04-03 09:47:29 +00:00
Sarah Griffiths
999fb4e44a Merge branch 'tag' into 'dev' 
Tag v1.1.1

See merge request epi2melabs/workflows/wf-transcriptomes!163
 2024-03-05 11:47:23 +00:00
Sarah Griffiths
bd5c89efc5 Tag v1.1.1 2024-03-05 11:47:23 +00:00
Sarah Griffiths
914c4a0c58 Merge branch 'CW-3516' into 'dev' 
Remove need to retry based on GTF/GFF

Closes CW-3516

See merge request epi2melabs/workflows/wf-transcriptomes!162
 2024-02-22 09:34:39 +00:00
Sarah Griffiths
6a14a1d85b Remove need to retry based on GTF/GFF 2024-02-22 09:34:38 +00:00
Sam Nicholls
05b3f3363b Merge branch 'CW-3532' into 'dev' 
Improve ref annotation transcript id version handling

Closes CW-3532

See merge request epi2melabs/workflows/wf-transcriptomes!160
 2024-02-19 10:29:04 +00:00
Sarah Griffiths
e3b1967872 Improve ref annotation transcript id version handling 2024-02-19 10:29:04 +00:00
Matt Parker
f3e2c964f3 Merge branch 'CW-3464' into 'dev' 
DE_analysis params change input types to numeric

See merge request epi2melabs/workflows/wf-transcriptomes!161
 2024-02-16 10:23:15 +00:00
Sarah Griffiths
e30d3aec98 DE_analysis params change input types to numeric 2024-02-16 10:23:15 +00:00
Neil Horner
9d0c835fbf Merge branch 'CW-3468_incorrect_ids' into 'dev' 
Resolve CW-3468 "Incorrect ids"

Closes CW-3468

See merge request epi2melabs/workflows/wf-transcriptomes!157
 2024-02-13 08:48:21 +00:00
Neil Horner
bb9acf55be Resolve CW-3468 "Incorrect ids" 2024-02-13 08:48:21 +00:00
Neil Horner
4f671051c1 Merge branch 'CW-3334_jaffa_mem' into 'dev' 
JAFFAL resources

Closes CW-3334

See merge request epi2melabs/workflows/wf-transcriptomes!155
 2024-02-12 15:25:19 +00:00
Neil Horner
d5b0cc6203 JAFFAL resources 2024-02-12 15:25:19 +00:00
Sarah Griffiths
f025538f17 Merge branch 'resource-updates' into 'dev' 
Resource updates

Closes CW-3362

See merge request epi2melabs/workflows/wf-transcriptomes!156
 2024-02-12 10:20:04 +00:00
Sarah Griffiths
4bb02049ec Resource updates 2024-02-12 10:20:02 +00:00