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909 commits

Author SHA1 Message Date
lquayle88
e7ac3ecd19 Modified resource requests in sbc_sharc.config for sarek 2022-10-02 00:24:39 +01:00
lquayle88
9b451b53b7 Increased cpus and memory for GATK4_MARKDUPLICATES in sbc_sharc.config for sarek 2022-10-01 23:31:51 +01:00
lquayle88
10c1490265 Increased memory and time for GATK4_MARKDUPLICATES in sbc_sharc.config for sarek 2022-10-01 23:15:13 +01:00
lquayle88
dbb3b3b44b Reinstated maxRetries and increased memory for GATK4_MARKDUPLICATES in sbc_sharc.config for sarek 2022-10-01 07:45:28 +01:00
lquayle88
8103718389 Reduced maxRetries upon error in sbc_sharc.config for sarek 2022-09-30 16:54:48 +01:00
Lewis Quayle
1eea9b464a
Merge branch 'nf-core:master' into sbc_sharc 2022-09-28 10:49:05 +01:00
Bruno Grande
735df9ef76
Merge branch 'master' into bgrande/sage-improve-downloads 2022-09-26 10:22:27 -07:00
Patrick Hüther
51ae760889
Merge pull request #413 from phue/biohpc_charliecloud_patch
biohpc_gen: update required modules
2022-09-25 23:28:04 +02:00
Lewis Quayle
e89114df8d
Merge branch 'nf-core:master' into sbc_sharc 2022-09-23 17:02:29 +01:00
lquayle88
c42a5a9a94 Updated resources requested by pipelines 2022-09-23 17:01:58 +01:00
lquayle88
ab1ad832df Updated resource requests for compatibility with high memory nodes 2022-09-23 13:18:50 +01:00
Simon Pearce
17c3767fef
Update crukmi.config
Fix the singularity cache dir and add process_single.
2022-09-23 12:53:54 +01:00
Lewis Quayle
7541ffb666
Merge branch 'nf-core:master' into sbc_sharc 2022-09-23 11:09:28 +01:00
lquayle88
7e34beb3c9 Updated resource requests for compatibility with general worker nodes 2022-09-23 11:08:39 +01:00
Adrija Kalvisa
7959b14385
Merge branch 'nf-core:master' into master 2022-09-22 13:15:32 +02:00
Austyn Trull
5400df135d
Merge pull request #412 from nf-core/cheaha_env_variable_updates
Fix cheaha config due to use of incorrect variable
2022-09-21 13:38:24 -05:00
lquayle88
1471257aaf Modified config for job submit rate 2022-09-20 19:51:31 +01:00
Lewis Quayle
9ee0bdc580
Merge branch 'nf-core:master' into sbc_sharc 2022-09-19 16:36:04 +01:00
lquayle88
adc88cfa1f Added config for limiting queue size and job submit rate 2022-09-19 16:30:30 +01:00
Patrick Hüther
85aa6adeed
Merge branch 'master' into biohpc_charliecloud_patch 2022-09-18 12:52:33 +02:00
ggabernet
c709be3b59 update cfc config maintenance 2022-09-18 12:06:37 +02:00
Bruno Grande
8bb9361359 Improve reliability of file transfers 2022-09-17 10:14:04 -07:00
lquayle88
55971bb94d Modularised error handling strategy to per pipeline basis 2022-09-16 17:29:08 +01:00
James A. Fellows Yates
ec638e62de
Apply suggestions from code review
Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
2022-09-15 09:10:29 +02:00
James A. Fellows Yates
b8751af6c6
Update conf/pipeline/mag/eva.config 2022-09-14 16:17:17 +02:00
James Fellows Yates
c0effc0366 Add HKI profile files 2022-09-14 15:34:27 +02:00
James A. Fellows Yates
8ea01e2041
Merge branch 'nf-core:master' into master 2022-09-14 15:01:34 +02:00
James A. Fellows Yates
3fcf708134
Merge pull request #414 from sheffield-bioinformatics-core/sbc_sharc
Added global institutional and pipeline configs for sbc_sharc
2022-09-14 11:46:41 +02:00
lquayle88
91bfa7341f Made changes requested for PR 2022-09-14 08:42:40 +01:00
Bruno Grande
3d3ee391be Limit the number of parallel transfers 2022-09-13 13:15:30 -07:00
lquayle88
9fef35d7d3 Updated pipeline configs for atacseq and chipseq 2022-09-13 17:08:56 +01:00
lquayle88
a9b62c53e0 Added global institutional and pipeline configs for sbc_sharc 2022-09-13 17:02:44 +01:00
Bruno Grande
abae5c4bd8 Decrease AWS Batch queue size 2022-09-12 11:40:43 -07:00
phue
b20f28a3c9 biohpc_gen: load charliecloud from lrz software tree and remove conda fallback
the biohpc_gen specific software tree is less maintained and outdated
2022-09-05 11:25:33 +02:00
Bruno Grande
80831358f9
Merge branch 'master' into bgrande/sage-aws 2022-09-01 13:21:36 -07:00
Lara Ianov
8448bb9a1e
re-define TMPDIR 2022-09-01 10:12:07 -05:00
Simon Pearce
2c738cae33
Update crukmi.config 2022-09-01 11:24:11 +01:00
Simon Pearce
a8faeda141
Update crukmi.config 2022-09-01 11:23:07 +01:00
SPearce
800931bff2 Add Sarek specific config 2022-09-01 11:13:23 +01:00
Simon Pearce
ba1d3f24cc
Update crukmi.config 2022-09-01 11:07:14 +01:00
Simon Pearce
81768e16a9
Merge branch 'nf-core:master' into crukmi 2022-09-01 10:20:25 +01:00
Simon Pearce
14a97ad0e8
Merge branch 'master' into crukmi 2022-09-01 10:07:24 +01:00
James Fellows Yates
b22e8b79c7 Fix cheaha config due to use of environmental variable 2022-09-01 11:01:23 +02:00
Kalayanee Chairat
9681716205
Update adcra.config
Fixing typo
2022-09-01 15:11:18 +07:00
Kalayanee Chairat
700f14d828
Merge pull request #1 from nf-core/master
Merging from master
2022-09-01 15:07:43 +07:00
Simon Pearce
864da0b5be
Merge branch 'master' into crukmi 2022-08-31 18:19:47 +01:00
Bruno Grande
9a37404a04
Merge branch 'master' into bgrande/sage-aws 2022-08-31 09:22:07 -07:00
Bruno Grande
179b343bd2 Incorporate resource limits 2022-08-31 09:18:27 -07:00
Bruno Grande
c883723559 Simplify resource adjustments 2022-08-31 09:10:30 -07:00
SPearce
1e1ca1e96b Incorporating executor options 2022-08-31 15:35:57 +01:00