911 commits

Author	SHA1	Message	Date
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
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