432 commits

Author	SHA1	Message	Date
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
AdrijaK	798d845a0d	run prettier	2022-09-22 14:21:02 +02:00
Adrija Kalvisa	7959b14385	Merge branch 'nf-core:master' into master	2022-09-22 13:15:32 +02:00
Patrick Hüther	85aa6adeed	Merge branch 'master' into biohpc_charliecloud_patch	2022-09-18 12:52:33 +02:00
Bruno Grande	8bb9361359	Improve reliability of file transfers	2022-09-17 10:14:04 -07:00
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 Fellows Yates	c0effc0366	Add HKI profile files	2022-09-14 15:34:27 +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
Lewis Quayle	61ae463606	Updated sbc_sharc.md	2022-09-13 17:13:57 +01:00
lquayle88	a9b62c53e0	Added global institutional and pipeline configs for sbc_sharc	2022-09-13 17:02:44 +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 the biohpc_gen specific software tree is less maintained and outdated	2022-09-05 11:25:33 +02:00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
SPearce	a142ad7eae	Added link to Sarek specific documentation	2022-09-01 13:55:08 +01:00
Simon Pearce	14a97ad0e8	Merge branch 'master' into crukmi	2022-09-01 10:07:24 +01:00
ameynert	28e59e38b4	Run prettier	2022-09-01 09:28:05 +01:00
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	c883723559	Simplify resource adjustments	2022-08-31 09:10:30 -07:00
Annick Renevey	0851903f66	include new config in pipeline configs file	2022-08-31 14:19:07 +02:00
Austyn Trull	90f638d376	Updating the cheaha documentation to clarify that /data/temporary-scratch/atrull will be used as storage for files that would normally go into one of the temporary locations when using Singularity	2022-08-29 10:47:46 -05:00
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
SPearce	d0662a3acb	Ran prettier	2022-08-15 09:33:30 +01:00
SPearce	a97b887d93	Written a help file	2022-08-12 16:57:04 +01:00
SPearce	0bfedde296	Initial attempt at a CRUKMI config file	2022-08-12 15:43:22 +01:00
Gwenna Breton	0e4f2b40d3	Added email of IT group	2022-08-08 16:14:17 +02:00
Gwenna Breton	2740b5efbf	Update docs/medair.md ... Fixed typo Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>	2022-08-08 16:08:05 +02:00
Gwenna Breton	648025c1ce	Clarified where to store singularity images	2022-08-08 16:04:21 +02:00
Gwenna Breton	6aa78833c3	Merge branch 'master' into medair	2022-08-01 16:46:55 +02:00
Matthieu Muffato	dda1d810b1	Latest stable version (rather than an edge one)	2022-07-20 14:35:39 +01:00
Matthieu Muffato	1ee20f0bb0	2 cores should be enough for the nextflow manager itself	2022-07-20 14:35:22 +01:00
Matthieu Muffato	60dc451569	The oversubscribed queue is recommended for workflow managers	2022-07-20 14:34:59 +01:00
Matthieu Muffato	1f1a9ac5f0	ISG provide the module, not the pathogen informatics team	2022-07-20 14:34:25 +01:00
Matthieu Muffato	2aad355fbf	The config doesn't mandate Singularity any more (Conda is fine too)	2022-07-20 14:32:43 +01:00
Priyanka Surana	fd87fbcb9d	Sanger profile update	2022-07-20 13:22:51 +01:00
qlr900	ff55ec67b4	update to current java+nextflow module combination	2022-07-07 14:30:48 +02:00
Gwenna Breton	6b9cdc8ef3	Added info about Sentieon singularities	2022-07-07 14:24:15 +02:00
Gwenna Breton	746db14d47	Update medair.md ... - updated text about storing singularity images - updated text about using profiles	2022-07-07 11:42:46 +02:00
qlr900	d19d6c0ae0	update wording	2022-07-06 16:19:16 +02:00
qlr900	4f98876429	add export to NXF_SINGULARITY_CACHEDIR	2022-07-06 13:35:10 +02:00
qlr900	f45b8645f6	update wording	2022-07-06 13:05:13 +02:00
qlr900	8a781b6bb2	modify alternative module load	2022-07-06 12:54:07 +02:00
qlr900	7ac08a1015	add alternative module load	2022-07-06 12:42:14 +02:00
Gwennid	96fd2bf217	Fixed formatting	2022-07-06 11:42:05 +02:00
Gwenna Breton	1d13dd9fbc	Changed where cgg-it is mentioned	2022-07-06 11:24:03 +02:00