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