kfukuta/wf-transcriptomes-v202
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309 Commits 1 Branch 1 Tag 73 MiB
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Author SHA1 Message Date
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
Sarah Griffiths
045a077fe1 docs update 2023-12-01 12:36:33 +00:00
Sarah Griffiths
26a78df739 Merge branch 'tag-v0.4.2' into 'dev' 
tag v0.4.2

See merge request epi2melabs/workflows/wf-transcriptomes!140
 2023-11-17 10:06:36 +00:00
Sarah Griffiths
b870078142 tag v0.4.2 2023-11-17 10:06:36 +00:00
Sarah Griffiths
7f5fe27bc2 Merge branch 'CW-2891' into 'dev' 
control for sample sheet

Closes CW-2891

See merge request epi2melabs/workflows/wf-transcriptomes!139
 2023-10-25 10:41:08 +00:00
Sarah Griffiths
e1b2a08918 control for sample sheet 2023-10-25 10:41:08 +00:00
Sam Nicholls
3fdef39c90 Merge branch 'update-template' into 'dev' 
Template updates [CW-1564][CW-2303][CW-2855]

See merge request epi2melabs/workflows/wf-transcriptomes!137
 2023-10-16 14:17:32 +00:00
Sam Nicholls
bb99170130 Template updates [CW-1564][CW-2303][CW-2855] 2023-10-16 14:17:32 +00:00
Neil Horner
0a8fe19e7c Merge branch 'container_pychop_2.7.9' into 'dev' 
Container pychop 2.7.9

See merge request epi2melabs/workflows/wf-transcriptomes!135
 2023-10-04 17:23:33 +00:00
Neil Horner
8aa2a74437 Container pychop 2.7.9 2023-10-04 17:23:33 +00:00
Neil Horner
c9f3b8da4a Merge branch 'container_pychop_2.7.9' into 'dev' 
Container pychop 2.7.9

See merge request epi2melabs/workflows/wf-transcriptomes!134
 2023-10-04 16:23:32 +00:00
Neil Horner
25d2bfd07c Container pychop 2.7.9 2023-10-04 16:23:32 +00:00
Sarah Griffiths
82610c7f69 Merge branch 'tag' into 'dev' 
tag

See merge request epi2melabs/workflows/wf-transcriptomes!133
 2023-09-28 08:18:12 +00:00
Sarah Griffiths
fb6182c717 tag 2023-09-28 08:18:11 +00:00
Sarah Griffiths
6f1e00aa2a Merge branch 'CW-2769' into 'dev' 
CW-2769 remove denovo

Closes CW-2769

See merge request epi2melabs/workflows/wf-transcriptomes!132
 2023-09-27 08:02:00 +00:00
Sarah Griffiths
f683d44411 CW-2769 remove denovo 2023-09-27 08:02:00 +00:00