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Author SHA1 Message Date
James Fellows Yates
f41cb5986f remove from testing 2021-08-20 10:18:04 +02:00
James Fellows Yates
59af7f0eee Delete SHH profiles due to decommissioning 2021-08-20 10:15:39 +02:00
James A. Fellows Yates
6701354060
Add genotyping_ug to SGE fixes 2021-08-20 10:11:11 +02:00
James A. Fellows Yates
5c9896b687
Merge pull request #265 from jfy133/eva-eager-subprofiles 
eva/eager: Try new strategy for SGE and Java incompatibility
 2021-08-04 10:43:14 +02:00
James Fellows Yates
b0e344846d Changes after code review from @aidaanva 2021-08-04 10:37:49 +02:00
James Fellows Yates
76fc461670 Try new strategy for SGE/JAVA bs 2021-08-04 10:14:56 +02:00
Rogan Grant
f793ffaace Updated iGenomes location 2021-08-03 15:10:54 -05:00
James A. Fellows Yates
0c3428f5d1
Merge pull request #263 from jfy133/master 
eager @ eva
 2021-08-03 14:20:50 +02:00
James A. Fellows Yates
00491de038
Update eva.config 2021-08-03 13:54:14 +02:00
Rogan Grant
079258ebbb
Minor text edits 2021-07-29 11:38:40 -05:00
Rogan Grant
482478878d Added instructions for module loading 2021-07-28 18:11:10 -05:00
Rogan Grant
24a2949fe2 Had executor options in wrong spot :( 2021-07-28 18:05:45 -05:00
Rogan Grant
6862fb8bfd testing ternary operatory 2021-07-28 18:01:03 -05:00
Rogan Grant
bcc69fe83c Enable use of himem nodes 2021-07-28 17:54:51 -05:00
Rogan Grant
ac11ca5568 Remove echo used for testing 2021-07-28 16:48:08 -05:00
Rogan Grant
3dd4f16d09 Added indicator for testing 2021-07-28 14:01:12 -05:00
Rogan Grant
09ed4d54b9 Just make command a single line for simplicity 2021-07-28 13:52:26 -05:00
Rogan Grant
09e0ea2674 typo 2021-07-28 13:46:40 -05:00
Rogan Grant
e1e0810d1b Clean up module loading script 2021-07-28 13:44:48 -05:00
Rogan Grant
e2c566ed13 Testing "automounts" 2021-07-28 13:38:06 -05:00
Rogan Grant
f104250ff4 Removed comment 2021-07-28 13:34:49 -05:00
Rogan Grant
9df267a192 Merged duplicate params 2021-07-28 13:27:17 -05:00
Rogan Grant
ff6823ec1d removed unnecessary space 2021-07-28 13:22:52 -05:00
Rogan Grant
9957e9eea1 Version 1 of custom config with queue-switching for long jobs and module loading 2021-07-28 13:11:02 -05:00
Rogan Grant
30ca555060 Added nu_genomics to list 2021-07-28 13:10:35 -05:00
Rogan Grant
e28a836702 Added nu_genomics to list 2021-07-28 13:10:18 -05:00
Rogan Grant
40170632aa First draft of markdown file, with instructions for installing nextflow and getting access 2021-07-28 13:04:32 -05:00
Rogan Grant
2af0f4a774 Added link to NU Genomics markdown 2021-07-28 13:03:59 -05:00
BarryDigby
732c3cfe7d
Merge pull request #262 from BarryDigby/master 
NUIG config
 2021-07-28 13:00:50 +01:00
Barry digby
2c6b9176e2 Merge branch 'master' of github.com:BarryDigby/configs 2021-07-28 12:19:45 +01:00
Barry digby
ef6b13e377 tabs rm 2021-07-28 12:19:11 +01:00
BarryDigby
871b82f6f4
Merge branch 'master' into master 2021-07-28 12:16:16 +01:00
Barry digby
f62298d211 w 2021-07-28 11:44:06 +01:00
Barry digby
2fc8082aad w 2021-07-28 11:43:39 +01:00
Barry digby
11cb6cc70d w 2021-07-28 11:41:42 +01:00
Barry digby
380adf083a markdowwwwn 2021-07-28 11:41:16 +01:00
Maxime U. Garcia
f82da1de71
Merge pull request #261 from maxulysse/master_cambridge 
fix: closes #260 + sort some lines
 2021-07-28 10:10:39 +02:00
Barry digby
70b2644c9a . 2021-07-27 17:39:37 +01:00
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