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Author SHA1 Message Date
Barry digby
2a06d956b3 mdlint so picky : ( 2021-07-27 17:18:42 +01:00
Barry digby
b7c7115f1e lll 
Merge branch 'nf-core-master'
 2021-07-27 17:13:58 +01:00
Barry digby
2b6e80561a Merge branch 'master' of https://github.com/nf-core/configs into 2021-07-27 17:13:17 +01:00
Barry digby
4f962260d0 s 2021-07-27 17:08:53 +01:00
Barry digby
04c0da5a2f nuig confg (lugh) 2021-07-27 17:05:27 +01:00
MaxUlysse
895c4eb610 fix: closes #260 + sort some lines 2021-07-27 16:35:19 +02:00
Harshil Patel
6ede44b221
Merge pull request #258 from ameynert/master 
Update eddie config docs & added viralrecon config
 2021-07-22 15:14:54 +01:00
ameynert
2112168420
Set BLASTDB_LMDB_MAP_SIZE 
This environment variable needs to be set in order to prevent memory allocation errors in the MAKEBLASTDB process.
 2021-07-22 15:07:19 +01:00
ameynert
17fad9dd15
Update pipeline/viralrecon.config 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-07-21 12:27:09 +01:00
ameynert
d9abb7d59f
Added eddie config to viralrecon 2021-07-21 12:23:47 +01:00
ameynert
5224eb5574
Updated resources folder & institute name 
Local resources folder was re-organized & re-named BioinformaticsResources. Added note about viralrecon & atacseq pipeline-specific config. IGMM name-changed recently; updated to IGC.
 2021-07-21 12:15:17 +01:00
ameynert
4ceb369af5
eddie.config for viralrecon pipeline 2021-07-21 12:10:43 +01:00
ameynert
0da2c57784
Merge pull request #4 from nf-core/master 
Merge from nf-core/configs
 2021-07-21 12:09:32 +01:00
Maxime U. Garcia
47217cae5b
Merge pull request #231 from maxulysse/master_kraken 
Remove kraken profile
 2021-07-20 09:29:47 +02:00
Maxime U. Garcia
30e058abf0
Merge branch 'master' into master_kraken 2021-07-20 09:26:56 +02:00
Harshil Patel
836d3c4015
Merge pull request #257 from drpatelh/V1200 
Add ARTIC v1200 primers to genomes config for viralrecon
 2021-07-12 14:03:29 +01:00
Harshil Patel
962dca7a46 Add ARTIC v1200 primers to genomes config for viralrecon 2021-07-12 12:24:49 +01:00
Gisela Gabernet
435955ab20
Merge pull request #256 from ggabernet/master 
Add AWS tower config
 2021-07-03 16:54:59 +02:00
ggabernet
e6f1bfaa1a finally add profile 2021-07-03 15:13:10 +02:00
ggabernet
68e12f85ec fix cchecker 2021-07-03 15:11:51 +02:00
ggabernet
2a69b90be6 fix cchecker 2021-07-03 15:09:43 +02:00
ggabernet
6475671c38 test that it fails 2021-07-03 14:57:58 +02:00
ggabernet
926f3ba24f update checker script 2021-07-03 14:52:44 +02:00
ggabernet
79fffbd77f update changes 2021-07-03 14:39:17 +02:00
ggabernet
f3274c49b5 test profile multiline 2021-07-03 14:36:56 +02:00
Gisela Gabernet
e2088a008d
Merge branch 'master' into master 2021-07-03 12:24:42 +02:00
ggabernet
f8690d49e8 add to tests 2021-07-03 12:21:03 +02:00
ggabernet
ee2e8392ab add aws_tower profile 2021-07-03 12:17:21 +02:00
Harshil Patel
69f63a006d
Merge pull request #254 from drpatelh/articv4 
Add ARTIC v4 primers to genomes config for viralrecon
 2021-07-01 12:31:02 +01:00
Gisela Gabernet
aae0f0bf07
Merge pull request #255 from ggabernet/master 
update cfc configs
 2021-07-01 10:59:25 +02:00
ggabernet
d59d099fe8 remove load module in cfc configs 2021-07-01 10:52:54 +02:00
James A. Fellows Yates
9298b353f5
Merge pull request #253 from jfy133/eva 
eager@EVA fixes more SGE + java silliness
 2021-06-29 12:53:34 +02:00
James A. Fellows Yates
5f4b915ae8
Update eva.config 2021-06-29 11:31:00 +02:00
ameynert
85c3f07f3c
Merge pull request #3 from nf-core/master 
Merge in from nf-core/configs
 2021-06-25 10:39:18 +01:00
Harshil Patel
93cfc48afd Add ARTIC v4 primers to genomes config 2021-06-21 21:04:16 +01:00
Edmund Miller
3019035fdb
Merge pull request #252 from Emiller88/utd_sysbio 
Add UTD sysbio
 2021-06-17 14:36:30 +00:00
Edmund Miller
cb213a499c
ci: Another missing comma 2021-06-17 09:34:03 -05:00
Edmund Miller
5ad959a436
fix(sysbio): Missing comma 2021-06-17 09:18:45 -05:00
Edmund Miller
f9e4ec4a8d
fix(sysbio): Add sysbio to rnaseq 2021-06-17 09:18:45 -05:00
Edmund Miller
21e1037e0c
docs(sysbio): Add rnaseq specific docs 2021-06-17 09:18:45 -05:00
Edmund Miller
e35c5fd1d8
fix(sysbio): Add nf-core params 2021-06-17 08:32:31 -05:00
Edmund Miller
41ae99d34a
feat(sysbio): Add cleanup 2021-06-17 08:17:55 -05:00
Edmund Miller
87c8e346e0
fix(sysbio): Change filetype 2021-06-17 08:14:48 -05:00
Edmund Miller
14a2106c63
fix(sysbio): Move rnaseq specific things to pipeline config 2021-06-17 08:14:48 -05:00
phue
45213cf6db add note about upcoming upstream fix 
also refactor the closure to make it slightly more readable
 2021-06-17 11:12:36 +02:00
Edmund Miller
7ff1c6cc7d
ci: Add sysbio 2021-06-16 21:19:49 -05:00
Edmund Miller
2a958f5ce3
docs: Add sysbio 2021-06-16 21:19:38 -05:00
Edmund Miller
472082254a
fix(sysbio): Add Star resources 2021-06-16 21:18:48 -05:00
Edmund Miller
b11f137901
fix(sysbio): Leave igenomes unfinished 2021-06-16 21:18:28 -05:00
Edmund Miller
04d0b27e81
fix(sysbio): Reduce memory on high processes 2021-06-16 21:17:40 -05:00