947 commits

Author	SHA1	Message	Date
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
ameynert	9167e81214	Added other Java processes with memory overhead, sorted alphabetically	2022-09-14 09:07:09 +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
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
ameynert	91ef9a3241	Added another Java process with overhead	2022-09-13 09:27:13 +01:00
Bruno Grande	abae5c4bd8	Decrease AWS Batch queue size	2022-09-12 11:40:43 -07:00
ameynert	a808933da8	Added another Java process that needs memory overhead	2022-09-09 08:37:21 +01:00
ameynert	29a0b30d85	Updated process names to Sarek 3	2022-09-07 16:00:52 +01:00
ameynert	d84754d328	Merge pull request #5 from nf-core/master ... Merge in from base repository	2022-09-07 15:45:08 +01:00
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 the biohpc_gen specific software tree is less maintained and outdated	2022-09-05 11:25:33 +02:00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
Annick Renevey	51871ea6fc	rnafusion setup for hasta usage	2022-08-31 11:32:01 +02:00
Lara Ianov	08b62ede83	Merge pull request #404 from nf-core/cheaha_singularity_update ... Cheaha Config Update	2022-08-30 14:45:50 -05:00
James A. Fellows Yates	c70a95f9c9	Merge branch 'master' into patch-2	2022-08-29 08:23:31 +02:00
Bruno Grande	9c8cb71bc7	Merge branch 'master' into bgrande/sage-aws	2022-08-25 16:29:20 -07:00
Bruno Grande	317e5a16cb	Improve AWS-related config for Sage profile	2022-08-25 16:24:52 -07:00
kalayaneech	93c4ba67a0	adding adcra configuration	2022-08-25 16:17:09 +07:00
Harshil Patel	8b9661825b	Replace NC_063383.1 fasta and gff and add Nextclade config	2022-08-24 15:21:44 +01:00
Harshil Patel	8dcfcfd856	Add monkeypox genome files to viralrecon genome config file	2022-08-24 12:13:17 +01:00
Austyn Trull	8d5ae4c3ab	Committing changes made by Brandon Wilk so that singularity containers will use scratch space	2022-08-23 15:30:13 -05:00
Ramprasad Neethiraj	9182b55acc	Merge branch 'master' into feat/hasta_update	2022-08-23 11:21:58 +02:00
Ramprasad Neethiraj	7ff2977a29	Merge branch 'master' of github.com:nf-core/configs into feat/hasta_update	2022-08-18 15:58:56 +02:00
Ramprasad Neethiraj	dd63dee7aa	update conf	2022-08-18 15:56:41 +02:00
Ramprasad Neethiraj	1c942759ea	update sentieon	2022-08-18 15:52:31 +02:00
Ramprasad Neethiraj	a6cce4ab6a	Merge branch 'master' into feat/hasta_java_memory_fix	2022-08-18 13:36:08 +02:00
SPearce	8ae3cba5e3	Reduce MPILEUP to 5GB	2022-08-15 11:35:59 +01:00
SPearce	0bfedde296	Initial attempt at a CRUKMI config file	2022-08-12 15:43:22 +01:00
Gwenna Breton	ffefefe0ab	Added contact emails	2022-08-08 16:11:55 +02:00
Gwenna Breton	6aa78833c3	Merge branch 'master' into medair	2022-08-01 16:46:55 +02:00
James A. Fellows Yates	0b47849532	Update mpcdf.config	2022-07-27 14:23:29 +02:00
Priyanka Surana	58508c4fbc	Sanger profile update	2022-07-20 13:14:42 +01:00
Nicolas Vannieuwkerke	f40825ac14	lower submission rate for vsc_ugent	2022-07-14 15:50:50 +02:00
Harshil Patel	2ab126fa4d	Update default Nextclade dataset to 2022-06-14T12:00:00Z	2022-07-11 18:28:41 +01:00
Gwenna Breton	4538e8aa36	Update medair.config ... - added path to singularity image for Sentieon - harmonized alignment	2022-07-07 13:41:42 +02:00
qlr900	d2b6b07de8	remove comments for mnaseseq	2022-07-06 14:18:31 +02:00
Gwennid	b6e2d03a02	Added Singularity cache dir	2022-07-06 13:59:35 +02:00
qlr900	6939c6f003	lower queueSize to 5	2022-07-06 13:34:18 +02:00
qlr900	49e756d1bc	fix typos	2022-07-06 12:39:55 +02:00
qlr900	56026c5ac4	remove beforeScript	2022-07-06 09:52:51 +02:00
qlr900	65d7080921	add conf/ku_sund_dangpu.config	2022-07-05 11:17:49 +02:00
James A. Fellows Yates	a141ff626b	Merge branch 'master' into eva-java-correction	2022-07-04 13:35:50 +02:00
Gwenna Breton	b3a6e199ca	Merge branch 'nf-core:master' into medair	2022-07-01 17:02:56 +02:00
Nicolas Vannieuwkerke	8a74c517d4	Merge branch 'vsc-ugent-fix' of github.com:nvnieuwk/configs into vsc-ugent-fix	2022-07-01 16:16:22 +02:00
Nicolas Vannieuwkerke	1e34595280	removed queue size limit	2022-07-01 16:16:18 +02:00
nvnieuwk	5ff845cde7	Merge branch 'master' into vsc-ugent-fix	2022-07-01 16:10:45 +02:00
Nicolas Vannieuwkerke	fa949a069e	added queuesize	2022-07-01 16:01:19 +02:00
Nicolas Vannieuwkerke	abfa3f47f4	lowered the job submit rate of vsc_ugent	2022-07-01 15:55:44 +02:00
Gwenna Breton	bb35d8e5d1	Added conf file for medair	2022-06-30 11:42:36 +02:00
Bruno Grande	6f0d9e6c43	Complete check_max() move to global config	2022-06-23 10:10:28 -07:00
Bruno Grande	a19d79f6ff	Move check_max() to global config	2022-06-23 09:44:16 -07:00
Bruno Grande	1c7230cb08	Add Sage-specific Sarek config	2022-06-23 09:15:42 -07:00
Bruno Grande	37121faf4a	Fix typoe with label name	2022-06-22 14:37:43 -07:00
Bruno Grande	ecd898584d	Handle Sarek-specific max labels	2022-06-22 13:54:13 -07:00
Bruno Grande	c7093dee13	Reduce max_memory to fit on an instance	2022-06-16 12:37:32 -07:00
James A. Fellows Yates	51d057564f	Fix python related seg faults mag@eva	2022-06-15 15:40:42 +02:00
James Fellows Yates	ba8bffbdfd	Use env scope instead of beforescript for mag@eva	2022-06-15 15:39:36 +02:00
James Fellows Yates	d12d98fb2e	Merge branches 'master' and 'eva-java-correction' of github.com:jfy133/nf-core-configs into master	2022-06-15 15:38:35 +02:00
James Fellows Yates	acabcbd9e8	Use _JAVA_OPTIONS instead	2022-06-15 15:27:40 +02:00
James Fellows Yates	76b0d1dd85	Merge branch 'eva-java-correction' of github.com:jfy133/nf-core-configs into eva-java-correction	2022-06-15 15:22:25 +02:00
James Fellows Yates	58dd9d49c7	Move beforeScript exports to env scope	2022-06-15 15:21:20 +02:00
Emil Bertilsson	c8c795595a	Merge branch 'nf-core:master' into feat/hasta_java_memory_fix	2022-06-09 15:10:46 +02:00
Emil Bertilsson	72e995f326	Adds generic fix for java memory issue on slurm	2022-06-09 10:28:20 +02:00
Bruno Grande	2898736cbe	Add Sage Bionetworks nf-core configuration	2022-06-08 14:16:52 -07:00
Nicolas Vannieuwkerke	b6d38859f0	fix for singularity cache for vsc_ugent profile	2022-06-08 16:28:28 +02:00
Nicolas Vannieuwkerke	98eacf030d	fix for singularity cache for vsc_ugent profile	2022-06-08 16:27:48 +02:00
Andrew Frank	d8c2775976	Update google.config to fix custom VM memory error	2022-06-07 09:41:41 -04:00
Maxime U. Garcia	c08cb5e97e	Merge branch 'master' into varskip_designs	2022-06-07 11:58:49 +02:00
Maxime U. Garcia	3ab5261bdd	Merge branch 'master' into kevbrick-patch-1	2022-06-07 11:58:36 +02:00
Maxime U. Garcia	844d250011	Merge branch 'master' into eva-java-correction	2022-06-07 11:57:05 +02:00
Nicolas Vannieuwkerke	44e25830e4	update for vsc_ugent	2022-06-07 11:33:22 +02:00
James A. Fellows Yates	46fba9c597	Update eva.config	2022-06-03 21:10:48 +02:00
James A. Fellows Yates	05cc8a08f1	Update eva.config	2022-06-03 21:08:19 +02:00
Åshild J. Vågene	ed526530d2	Rename mjolnir_globe to mjolnir_globe.config	2022-06-03 17:15:12 +02:00
Åshild J. Vågene	22ed36a73d	cacheDir update	2022-06-03 15:33:58 +02:00
James Fellows Yates	9ef52af084	Increase overhead	2022-06-03 14:24:27 +02:00
James Fellows Yates	c40ebb9acf	Add overhead for get_software_versions	2022-06-03 14:21:41 +02:00
James Fellows Yates	df0429ce9d	Replace oracle specific _JAVA_OPTIONS to portable JAVA_TOOLS_OPTIONS	2022-06-03 14:20:39 +02:00
Phil Ewels	b51059a3ae	Merge branch 'master' into config_ucph-mjolnir_ash	2022-06-03 13:21:36 +02:00
Phil Ewels	3b338828d5	Merge branch 'master' into kevbrick-patch-1	2022-06-03 13:20:09 +02:00
James A. Fellows Yates	7353fb257d	Merge pull request #380 from jfy133/taxprofiler ... Add MAG @ EVA profile	2022-06-03 12:54:47 +02:00
James Fellows Yates	5a67eba04c	Add MAG @ EVA profile	2022-06-03 12:41:08 +02:00