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Author	SHA1	Message	Date
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	57f63add02	Merge pull request #417 from Sage-Bionetworks-Workflows/bgrande/sage-improve-downloads ... Improve reliability of file transfers with retries and reduced concurrency	2022-09-26 10:24:14 -07:00
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
James A. Fellows Yates	2b1141e9c9	Merge pull request #420 from SPPearce/crukmi ... Update crukmi.config	2022-09-23 15:14:43 +02:00
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
Martin Proks	0d4ecaeb6d	Merge pull request #419 from AdrijaK/master ... add config for KU_SUND_DANGPU	2022-09-23 10:29:00 +02:00
AdrijaK	798d845a0d	run prettier	2022-09-22 14:21:02 +02:00
Adrija Kalvisa	65b6bf7c62	add ku_sund_dangpu	2022-09-22 13:37:45 +02:00
Adrija Kalvisa	339a072884	fix typo	2022-09-22 13:35:42 +02:00
Adrija Kalvisa	55d7b3fc00	add KU SUND DANGPU ... add the profile for Dangpu server hosted by Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW)/ Novo Nordisk Foundation Center for Protein Research (CPR)	2022-09-22 13:35:08 +02:00
Adrija Kalvisa	5315ddd92f	add KU_SUND_DANGPU	2022-09-22 13:22:26 +02:00
Adrija Kalvisa	ce916bf4b5	fix typo	2022-09-22 13:21:10 +02:00
Adrija Kalvisa	2e9578498a	add ku_sund_dangpu.config	2022-09-22 13:20:42 +02:00
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
Gisela Gabernet	89dc3c429f	Merge pull request #418 from ggabernet/master ... update cfc config maintenance	2022-09-18 12:07:43 +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	c9c4d02f0d	Merge pull request #416 from jfy133/master ... Add HKI cluster	2022-09-15 09:18:00 +02:00
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
Maxime U. Garcia	326ab0036e	Merge pull request #415 from Sage-Bionetworks-Workflows/bgrande/sage-tweaks ... Adjust AWS-related configuration to improve reliability	2022-09-14 11:31:10 +02:00
lquayle88	be356eb400	Ran prettier on docs/sbc_sharc.md	2022-09-14 10:24:56 +01:00
lquayle88	32403b6222	Updated pipeline config docs for atacseq, chipseq and rnaseq	2022-09-14 08:46:11 +01:00
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
Lewis Quayle	61ae463606	Updated sbc_sharc.md	2022-09-13 17:13:57 +01:00
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	47fa890ad7	Merge pull request #407 from Sage-Bionetworks-Workflows/bgrande/sage-aws ... Improve AWS-related config for Sage profile	2022-09-01 13:29:49 -07:00
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