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Author SHA1 Message Date
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
Neil Horner
5d16332a2c Merge branch 'condition_sheet_docs' into 'dev' 
Removed reference to condition sheet

See merge request epi2melabs/workflows/wf-transcriptomes!131
 2023-09-20 12:18:11 +00:00
Neil Horner
f86024c4f8 Removed reference to condition sheet 2023-09-20 11:05:09 +01:00
Matt Parker
4f589b2008 Merge branch 'CW-2754-dead-links-readme' into 'dev' 
CW-2754-dead-links-readme

Closes CW-2754

See merge request epi2melabs/workflows/wf-transcriptomes!130
 2023-09-12 13:31:52 +00:00
Matt Parker
2da8b8286c CW-2754-dead-links-readme 2023-09-12 14:26:03 +01:00
Sarah Griffiths
7cd69ab26f Merge branch 'wrong-version' into 'dev' 
update version

See merge request epi2melabs/workflows/wf-transcriptomes!129
 2023-09-08 10:55:54 +00:00
Sarah Griffiths
7e2d0214e4 update version 2023-09-08 10:55:54 +00:00
Sarah Griffiths
57d4bf932d Merge branch 'CW-2680' into 'dev' 
deal with transcriptome fasta headers that contains |

Closes CW-2680

See merge request epi2melabs/workflows/wf-transcriptomes!124
 2023-09-06 20:18:40 +00:00
Sarah Griffiths
edf3a24315 deal with transcriptome fasta headers that contains | 2023-09-06 20:18:40 +00:00
Neil Horner
36d37a8d5f Merge branch 'CW-2700_demo_not_working' into 'dev' 
Resolve CW-2700 "Demo not working"

Closes CW-2700

See merge request epi2melabs/workflows/wf-transcriptomes!127
 2023-09-06 08:59:17 +00:00
Neil Horner
326f0910fc Resolve CW-2700 "Demo not working" 2023-09-06 08:59:17 +00:00
Sarah Griffiths
9447f7404d Merge branch 'params-fix' into 'dev' 
params update defaults

See merge request epi2melabs/workflows/wf-transcriptomes!128
 2023-09-06 08:00:10 +00:00
Sarah Griffiths
4065a4d82f params update defaults 2023-09-06 08:00:10 +00:00
Sarah Griffiths
68ff1931c5 Merge branch 'template-update' into 'dev' 
Update fastqingress.nf

See merge request epi2melabs/workflows/wf-transcriptomes!126
 2023-09-05 08:57:28 +00:00
Sarah Griffiths
2bda37388c Update fastqingress.nf 2023-09-05 08:57:28 +00:00
Sarah Griffiths
d9ee1034a3 Merge branch 'template-update' into 'dev' 
Update file check_sample_sheet.py

See merge request epi2melabs/workflows/wf-transcriptomes!125
 2023-09-04 09:24:15 +00:00
Sarah Griffiths
fb718ac3f7 Update file check_sample_sheet.py 2023-09-01 16:03:19 +00:00
Neil Horner
261437ad81 Merge branch 'CW-2674_docs' into 'dev' 
Fix typo

Closes CW-2674

See merge request epi2melabs/workflows/wf-transcriptomes!123
 2023-09-01 08:46:46 +00:00
Neil Horner
9e6654422e Fix typo 2023-08-31 22:52:18 +01:00
Neil Horner
3509cebde4 Merge branch 'gh26_typo' into 'dev' 
Fix typo

See merge request epi2melabs/workflows/wf-transcriptomes!122
 2023-08-11 15:23:16 +00:00
Neil Horner
816fe70b91 Fix typo 2023-08-11 15:34:42 +01:00
Sarah Griffiths
fcc7347a8b Merge branch 'common-sha-and-tag' into 'dev' 
common sha update and tag

See merge request epi2melabs/workflows/wf-transcriptomes!120
 2023-08-10 12:48:46 +00:00
Sarah Griffiths
2ce40ee2f0 common sha update and tag 2023-08-10 12:48:45 +00:00
Sarah Griffiths
1153e705fa Merge branch 'CW-2498' into 'dev' 
tidy up DE outputs

Closes CW-2498

See merge request epi2melabs/workflows/wf-transcriptomes!118
 2023-08-10 10:05:11 +00:00
Sarah Griffiths
ab850ac67f tidy up DE outputs 2023-08-10 10:05:11 +00:00
Sarah Griffiths
3a5de57317 Merge branch 'schema-5.1.1' into 'dev' 
add titles

See merge request epi2melabs/workflows/wf-transcriptomes!119
 2023-08-08 11:18:15 +00:00
Sarah Griffiths
d535778497 add titles 2023-08-08 11:18:15 +00:00
Sarah Griffiths
dd8466e62d Merge branch 'nextflow-version' into 'dev' 
nf version

See merge request epi2melabs/workflows/wf-transcriptomes!117
 2023-08-03 15:54:39 +00:00
Sarah Griffiths
b6159b2c26 nf version 2023-08-03 15:54:39 +00:00
Sarah Griffiths
838d19de45 Merge branch 'remove_transcriptoe_assembly_option' into 'dev' 
Remove unused parameter

See merge request epi2melabs/workflows/wf-transcriptomes!116
 2023-07-26 21:09:29 +00:00
Neil Horner
285e7c8ecf Remove unused parameter 2023-07-26 21:09:29 +00:00
Sarah Griffiths
e56aefe7db Merge branch 'CW-2362-no-gene-id' into 'dev' 
fix and test for files with no gene id in attributes

Closes CW-2362

See merge request epi2melabs/workflows/wf-transcriptomes!115
 2023-07-26 18:14:00 +00:00
Sarah Griffiths
ec3c346fd8 fix and test for files with no gene id in attributes 2023-07-26 18:14:00 +00:00
Sarah Griffiths
805c15297e Merge branch 'CW-2209-docs' into 'dev' 
CW-2209 docs remove =

Closes CW-2209

See merge request epi2melabs/workflows/wf-transcriptomes!114
 2023-07-25 09:51:34 +00:00