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1792 commits 4 branches 0 tags 1.9 MiB
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924 commits

Author SHA1 Message Date
Edmund Miller
0cabf67b61
feat(demultiplex): Add optimized transfers for bases2fastq 2022-10-05 17:21:23 -05:00
Lewis Quayle
755862fc61
Merge branch 'nf-core:master' into sbc_sharc 2022-10-05 19:55:43 +01:00
Giuseppe Martone
64fec62a6d
Merge branch 'master' into master 2022-10-04 22:59:17 +02:00
Giuseppe Martone
e37bccc9d8
Update tigem.config 2022-10-04 22:58:50 +02:00
Alexander Peltzer
a9781042c7
Merge pull request #392 from nf-core/custom-mag-eva 
Fix python related seg faults mag@eva
 2022-10-04 21:58:49 +02:00
Alexander Peltzer
0d8471a082
Merge pull request #421 from Puumanamana/master 
University of Hawaii at Manoa's HPCC config
 2022-10-04 21:56:40 +02:00
Alexander Peltzer
8b68ffce89
Merge branch 'master' into custom-mag-eva 2022-10-04 21:55:37 +02:00
Phil Ewels
e78d941105
Merge branch 'master' into ccga_beegfs_update 2022-10-04 14:18:51 +02:00
Marc Hoeppner
e5b798e21f Updating CCGA med to use the new Beegfs file system 2022-10-04 14:07:44 +02:00
Giuseppe Martone
ce39096f32
Create tigem.config 2022-10-04 10:44:19 +02:00
lquayle88
584052cfff Revised base and all pipeline configs to provide memory on per core basis 2022-10-04 09:12:29 +01:00
lquayle88
3f2ffa314d Revised base and sarek configs to provide memory on per core basis 2022-10-04 00:25:16 +01:00
Cedric
d429a59a0d
add automounts for singularity 2022-10-02 18:44:22 -10:00
Cedric Arisdakessian
c479780d8f create mana config 2022-10-03 03:38:20 +00:00
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