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230 commits

Author SHA1 Message Date
James A. Fellows Yates
bf658abc77
Update eva.config 2022-05-02 13:59:13 +02:00
James A. Fellows Yates
44238471cf
Update eva.config 2022-03-31 13:12:50 +02:00
James Fellows Yates
2277b541a3 Re-add bash bin specification 2022-03-31 11:06:53 +02:00
James A. Fellows Yates
8ad4ddac6a
Merge branch 'master' into fix-eva 2022-03-29 12:50:54 +02:00
James Fellows Yates
3d2a612b39 Remove setting of bash in clusterOotions 2022-03-29 12:48:37 +02:00
b97pla
9a6cdfc21e removed process-specific requirements for sarek, request miarka high-mem node 2022-03-24 14:25:43 +01:00
b97pla
5466d927f1 added requirements for uppmax cluster miarka 2022-03-23 15:29:40 +01:00
James A. Fellows Yates
1b5037ce5e
Update eva.config 2022-03-15 07:49:06 +01:00
James A. Fellows Yates
1565b2ce63
Update eva.config 2022-03-15 07:42:23 +01:00
James A. Fellows Yates
f725b6c431
Apply suggestions from code review 2022-03-15 07:36:34 +01:00
James A. Fellows Yates
4670f8bf0c
Update eva.config 2022-03-14 14:56:01 +01:00
James A. Fellows Yates
975fca6721
Apply suggestions from code review 2022-03-07 13:51:00 +01:00
James Fellows Yates
70318c3b2a Tweak eager settigs 2022-03-03 14:29:30 +01:00
ilight1542
5a0543e4ac
Merge branch 'rnaseq_mpcdf' into mpcdf_eager_config_update 2022-03-03 14:17:18 +01:00
ilight1542
25c644abb7 modified mpcdf configs (general + eager) 2022-03-03 13:55:02 +01:00
James A. Fellows Yates
17312604cf
Update mpcdf.config 2022-03-03 12:25:06 +01:00
James Fellows Yates
94f8cbcb84 Add rnaseq pipeline specific config for MPCDF 2022-03-03 12:20:02 +01:00
James A. Fellows Yates
5547e45ab5
Merge branch 'master' into jfy133-patch 2022-03-02 08:28:22 +01:00
James A. Fellows Yates
ea052a7b67
Merge pull request #334 from jfy133/eva-update
eva: generalise custom SGE mem flag
2022-03-01 09:23:04 +01:00
James A. Fellows Yates
46f046d477
Update eva.config 2022-02-28 14:00:37 +01:00
Mei Wu
dcba537d15 picard md is single threaded 2022-02-21 16:19:17 +01:00
Combiz Khozoie
2d434c6ee5
Merge pull request #321 from nf-core/combiz-patch-1
Imperial config updates
2022-02-11 14:49:30 +00:00
Maxime U. Garcia
4a936a685e
Merge pull request #317 from nf-core/praveenraj2018-patch-1
Added genome parameter
2022-02-11 15:33:18 +01:00
Combiz Khozoie
a77f718ae2
Merge pull request #330 from nf-core/master
Pulling master to branch
2022-02-11 14:18:01 +00:00
Harshil Patel
8fa6ab9b35
Merge pull request #323 from stevin-wilson/patch-1
Added ARTIC v4.1 primer set information
2022-02-10 19:17:47 +00:00
James Fellows Yates
88ddc9eee7 fffff 2022-02-10 11:34:57 +01:00
James Fellows Yates
d7d0f5cecc Change base time 2022-02-10 11:32:49 +01:00
James Fellows Yates
dbd78f8075 Re add . 2022-02-10 11:26:18 +01:00
James Fellows Yates
dd94895f16 remove quotes 2022-02-10 11:22:45 +01:00
James Fellows Yates
39c2d9b25b Oops 2022-02-10 11:19:16 +01:00
James Fellows Yates
c0ee3225ad Add times for 365d 2022-02-10 11:02:52 +01:00
Thiseas C. Lamnidis
fa4075c2a0
Removed all time limits 2022-02-10 10:00:18 +01:00
James A. Fellows Yates
2b06293f64
Read add empty BAM exit code for qualitmap 255 2022-02-08 11:15:17 +01:00
James A. Fellows Yates
8c5a54ac9f
Update conf/pipeline/eager/eva.config 2022-02-06 19:37:53 +01:00
James A. Fellows Yates
aa525c6ebf
Allow exit code 1 retry for all java processes 2022-02-06 09:07:53 +01:00
Stevin Wilson
dbb71161c5
Added ARTIC v4.1 primer set information 2022-02-04 15:31:51 -05:00
James A. Fellows Yates
81fe720b00
Update eva.config 2022-02-04 09:31:33 +01:00
James A. Fellows Yates
86a9042eac
Update eva.config 2022-02-04 09:25:01 +01:00
Combiz Khozoie
2bdf5863d9
Update imperial.config
Removed my contact details.  Users can request help on the nf-core slack.
2022-02-03 18:28:11 +00:00
James A. Fellows Yates
50aafc6410
Update eva.config 2022-02-03 17:03:10 +01:00
James A. Fellows Yates
e02196d6ad
Update eva.config 2022-02-03 17:02:34 +01:00
James A. Fellows Yates
0e41349324
Update eva.config 2022-02-03 17:01:54 +01:00
James Fellows Yates
2562a2f563 Remove virtual free 2022-02-02 08:06:00 +01:00
James A. Fellows Yates
8739aabbf0
Bump markduplicates by default 2022-02-02 08:00:13 +01:00
Harshil Patel
9792226f5c
Update genomes.config 2022-01-27 12:45:41 +00:00
Praveen Raj S
5c1afd56bf
Added genome parameter
Added genome parameter to the config file
2022-01-20 22:25:31 +01:00
Harshil Patel
cd6b8e0f17 Add --nextclade_dataset params 2022-01-17 16:51:55 +00:00
Harshil Patel
f26c465bd4 Add Nextclade genome details to viralrecon genome config 2022-01-17 11:27:10 +00:00
James A. Fellows Yates
5fd5c43906
Update eva.config 2022-01-14 07:03:05 +01:00
Maxime U. Garcia
61682f33b3
Merge pull request #310 from nf-core/praveenraj2018-patch-1
Updated sentieon version through a new module file
2022-01-10 12:04:20 +01:00