kfukuta/wf-transcriptomes-v202
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Author SHA1 Message Date
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
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