kfukuta/wf-transcriptomes-v202
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534 Commits

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Author SHA1 Message Date
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
Sarah Griffiths
08de000d12 CW-2209 docs remove = 2023-07-25 09:51:34 +00:00
Sarah Griffiths
941532588d Merge branch 'template-updates' into 'dev' 
template updates

See merge request epi2melabs/workflows/wf-transcriptomes!113
 2023-07-25 08:33:01 +00:00
Sarah Griffiths
a58d08b6c4 template updates 2023-07-25 08:33:01 +00:00
Sarah Griffiths
2a5ae64617 Merge branch 'CW-2217' into 'dev' 
CW-2217 fix ordering of sample_ids

Closes CW-2217

See merge request epi2melabs/workflows/wf-transcriptomes!112
 2023-07-12 11:05:34 +00:00
Sarah Griffiths
f86b74a494 CW-2217 fix ordering of sample_ids 2023-07-12 11:05:34 +00:00
Sarah Griffiths
25518e37c5 Merge branch 'tag-v0.1.14' into 'dev' 
tag v0.2.0

See merge request epi2melabs/workflows/wf-transcriptomes!111
 2023-07-12 08:21:12 +00:00
Sarah Griffiths
a3bc02888e tag v0.2.0 2023-07-12 08:21:11 +00:00
Sarah Griffiths
40b4277576 Merge branch 'CW-2313' into 'dev' 
CW-2313 remove condition sheet requirement

Closes CW-2313

See merge request epi2melabs/workflows/wf-transcriptomes!106
 2023-07-10 16:45:32 +00:00
Sarah Griffiths
df6c9a2a31 CW-2313 remove condition sheet requirement 2023-07-10 16:45:32 +00:00
Neil Horner
a246453164 Merge branch 'cw-2346' into 'dev' 
Hide jaffal_dir option

See merge request epi2melabs/workflows/wf-transcriptomes!109
 2023-07-04 12:56:09 +00:00
Sam Nicholls
8d6545b462 Hide jaffal_dir option 2023-07-04 11:31:51 +01:00
Neil Horner
53c933aac6 Merge branch 'add-util' into 'dev' 
Reconcile template

See merge request epi2melabs/workflows/wf-transcriptomes!110
 2023-07-04 10:13:05 +00:00
Sam Nicholls
542f822ca6 Reconcile template 2023-07-04 10:13:05 +00:00
Sarah Griffiths
ea2dde72df Merge branch 'CW-2308' into 'dev' 
CW-2308 remove real path use

Closes CW-2308

See merge request epi2melabs/workflows/wf-transcriptomes!107
 2023-06-28 17:37:49 +00:00
Sarah Griffiths
d0e7fc4b26 CW-2308 remove real path use 2023-06-28 17:37:49 +00:00
Sarah Griffiths
a730e13ac8 Merge branch 'CW-2307' into 'dev' 
CW-2307 ref_transcriptome default not null

Closes CW-2307

See merge request epi2melabs/workflows/wf-transcriptomes!108
 2023-06-28 15:19:41 +00:00
Sarah Griffiths
79d5821c14 CW-2307 ref_transcriptome default not null 2023-06-28 15:19:41 +00:00
Sarah Griffiths
cb34c14421 Merge branch 'cw-2283' into 'dev' 
GitHub issue templates [CW-2283]

See merge request epi2melabs/workflows/wf-transcriptomes!105
 2023-06-26 11:48:59 +00:00
Sam Nicholls
8206a3173c GitHub issue templates [CW-2283] 2023-06-20 19:18:00 +01:00
Neil Horner
14c6191766 Merge branch 'HELP-6233' into 'dev' 
Standardise parameters in readme

Closes HELP-6233

See merge request epi2melabs/workflows/wf-transcriptomes!104
 2023-06-16 10:08:48 +00:00
Neil Horner
99d43b48b9 Standardise parameters in readme 2023-06-16 10:08:48 +00:00
Sarah Griffiths
cb73e0a6cd Merge branch 'CW-2188-denovo-test' into 'dev' 
CW-2188 add test for denovo plus warnings

Closes CW-2188

See merge request epi2melabs/workflows/wf-transcriptomes!100
 2023-06-14 13:21:27 +00:00
Sarah Griffiths
9f449ae467 CW-2188 add test for denovo plus warnings 2023-06-14 13:21:27 +00:00
Neil Horner
7d3b67acfd Merge branch 'cw-2224' into 'dev' 
Update nextflowVersion to 22.10.8

See merge request epi2melabs/workflows/wf-transcriptomes!103
 2023-06-12 15:19:25 +00:00
Sam Nicholls
e359561703 Update nextflowVersion to 22.10.8 2023-06-12 11:28:39 +01:00
Neil Horner
775d13d5b6 Merge branch 'typo' into 'dev' 
Typo

See merge request epi2melabs/workflows/wf-transcriptomes!102
 2023-06-12 08:20:09 +00:00
Neil Horner
3ac202d457 Typo 2023-06-12 09:03:29 +01:00
Sarah Griffiths
fc642c9535 Merge branch 'template-update' into 'dev' 
wf-transcriptomes template update

See merge request epi2melabs/workflows/wf-transcriptomes!101
 2023-06-08 14:58:50 +00:00
Sarah Griffiths
61deb0715f wf-transcriptomes template update 2023-06-08 14:58:50 +00:00
Sarah Griffiths
12429039d3 Merge branch 'CW-1920-annotation-file-types' into 'dev' 
CW-1920-Annotation-file-types

Closes CW-1920

See merge request epi2melabs/workflows/wf-transcriptomes!97
 2023-05-31 20:48:35 +00:00
Sarah Griffiths
ab275b6440 CW-1920-Annotation-file-types 2023-05-31 20:48:35 +00:00
Sarah Griffiths
2b95323598 Merge branch 'mac-ci-not-jaffal' into 'dev' 
transcriptomes mac ci arm 64

See merge request epi2melabs/workflows/wf-transcriptomes!99
 2023-05-16 20:54:24 +00:00
Sarah Griffiths
1d5fcdd211 transcriptomes mac ci arm 64 2023-05-16 20:54:23 +00:00
Matt Parker
8c7aabb5d1 Merge branch 'cw-2098' into 'dev' 
Add AWS demo url configuration

See merge request epi2melabs/workflows/wf-transcriptomes!98
 2023-05-16 18:26:23 +00:00
Sarah Griffiths
970ffa9734 tag 2023-05-16 16:34:08 +00:00
Sam Nicholls
63bef44dcc Add AWS demo url configuration 2023-05-16 14:59:53 +01:00
Sarah Griffiths
fcefe9e138 Merge branch 'template-updates' into 'dev' 
template updates

See merge request epi2melabs/workflows/wf-transcriptomes!96
 2023-05-09 10:09:33 +00:00
Sarah Griffiths
5df7e3c2cd template updates 2023-05-09 10:09:33 +00:00
Sarah Griffiths
85e85409ef Merge branch 'tag' into 'dev' 
tag

See merge request epi2melabs/workflows/wf-transcriptomes!94
 2023-04-06 08:28:13 +00:00
Sarah Griffiths
a4c472062c tag 2023-04-06 08:28:13 +00:00
Sarah Griffiths
9ed8e34f6b Merge branch 'remove-mr-sha' into 'dev' 
remove MR sha

See merge request epi2melabs/workflows/wf-transcriptomes!93
 2023-04-04 15:58:21 +00:00
Sarah Griffiths
c3137f6ad6 remove MR sha 2023-04-04 13:11:54 +00:00