kfukuta/wf-transcriptomes-v202
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374 Commits 1 Branch 1 Tag 73 MiB
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374 Commits

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Author SHA1 Message Date
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
Sarah Griffiths
9cf89d4360 Merge branch 'CW-3075-b' into 'dev' 
Seperate DE files required for the report and to be output to the user

See merge request epi2melabs/workflows/wf-transcriptomes!159
 2024-02-09 21:45:22 +00:00
Sarah Griffiths
1c67e3274e Seperate DE files required for the report and to be output to the user 2024-02-09 21:45:22 +00:00
Neil Horner
46f748f493 Merge branch 'CW-2971_publish_table' into 'dev' 
Publish isoforms table

Closes CW-2971

See merge request epi2melabs/workflows/wf-transcriptomes!148
 2024-02-09 10:59:02 +00:00
Neil Horner
fdb938a147 Publish isoforms table 2024-02-09 10:59:01 +00:00
Sarah Griffiths
84dbafd1c9 Merge branch 'CW-3174' into 'dev' 
No ref annotation workflow still completes

Closes CW-3174

See merge request epi2melabs/workflows/wf-transcriptomes!154
 2024-02-07 22:50:04 +00:00
Sarah Griffiths
bf136640ed No ref annotation workflow still completes 2024-02-07 22:50:04 +00:00
Sarah Griffiths
077ad86a92 Merge branch 'CW-3075' into 'dev' 
CW-3075 improve counts output files

Closes CW-3075

See merge request epi2melabs/workflows/wf-transcriptomes!149
 2024-02-02 10:38:51 +00:00
Sarah Griffiths
1be77ba77f CW-3075 improve counts output files 2024-02-02 10:38:50 +00:00
Neil Horner
04e76d4271 Merge branch 'CW-3327_mapping_1_thread' into 'dev' 
Resolve CW-3327 "Mapping 1 thread"

Closes CW-3327

See merge request epi2melabs/workflows/wf-transcriptomes!151
 2024-01-18 19:40:14 +00:00
Neil Horner
f111755d12 Resolve CW-3327 "Mapping 1 thread" 2024-01-18 19:40:14 +00:00
Neil Horner
fbd1bf819c Merge branch 'demo_typo' into 'dev' 
Fix demo command

See merge request epi2melabs/workflows/wf-transcriptomes!152
 2024-01-17 15:16:07 +00:00
Neil Horner
b10ca2d9dc Fix demo command 2024-01-17 15:16:07 +00:00
Sarah Griffiths
58d7c7db5e Merge branch 'template_updates_2024-01-12' into 'dev' 
Template updates 2024 01 12

See merge request epi2melabs/workflows/wf-transcriptomes!150
 2024-01-16 11:48:09 +00:00
Neil Horner
92cb357edc Template updates 2024 01 12 2024-01-16 11:48:09 +00:00
Sarah Griffiths
a979ad1774 Merge branch 'temp-up' into 'dev' 
Temp up

See merge request epi2melabs/workflows/wf-transcriptomes!147
 2024-01-04 10:18:39 +00:00
Sarah Griffiths
07b9edcb99 Temp up 2024-01-04 10:18:39 +00:00
Sarah Griffiths
c66a48525f Merge branch 'example-cmd-again' into 'dev' 
example cmd update

See merge request epi2melabs/workflows/wf-transcriptomes!145
 2023-12-08 14:35:24 +00:00
Sarah Griffiths
45dc9efb49 example cmd update 2023-12-08 14:35:24 +00:00
Sarah Griffiths
6e5b1262ff Merge branch 'de_analysis_example_cmd' into 'dev' 
de_analysis include in sample cmd

See merge request epi2melabs/workflows/wf-transcriptomes!144
 2023-12-08 09:32:08 +00:00
Sarah Griffiths
3acf993586 de_analysis include in sample cmd 2023-12-08 09:32:07 +00:00
Sarah Griffiths
1a62c724b3 Merge branch 'template-tag' into 'dev' 
template update

See merge request epi2melabs/workflows/wf-transcriptomes!143
 2023-12-07 14:05:03 +00:00
Sarah Griffiths
ed847d9a1f template update 2023-12-07 14:05:02 +00:00
Sarah Griffiths
2580c99ae4 Merge branch 'CW-2369' into 'dev' 
Resolve CW-2369

Closes CW-2369

See merge request epi2melabs/workflows/wf-transcriptomes!138
 2023-12-05 18:42:47 +00:00
Neil Horner
d01162025a Resolve CW-2369 2023-12-05 18:42:47 +00:00
Sarah Griffiths
feed09c16c Merge branch 'CW-3127' into 'dev' 
pychopper parameters clear up

Closes CW-3127

See merge request epi2melabs/workflows/wf-transcriptomes!142
 2023-12-04 21:12:57 +00:00
Sarah Griffiths
35dc9dd722 pychopper parameters clear up 2023-12-04 21:12:57 +00:00
Sarah Griffiths
d8fe530905 Merge branch 'CW-3105' into 'dev' 
docs update

Closes CW-3105

See merge request epi2melabs/workflows/wf-transcriptomes!141
 2023-12-01 12:36:33 +00:00