410 commits

Author	SHA1	Message	Date
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 the biohpc_gen specific software tree is less maintained and outdated	2022-09-05 11:25:33 +02:00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
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
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
Gwenna Breton	235097e58e	Addressed review comments ... - removed mention of iGenomes - clarified whom to contact for support	2022-07-06 11:20:59 +02:00
Gwenna Breton	1d7a34b11f	Removed comment about internal doc	2022-07-06 11:17:58 +02:00
Gwenna Breton	b202ad70ac	Removed mention of specific module versions	2022-07-06 11:16:38 +02:00
Gwenna Breton	84174043e4	Added details for nf-core pipelines download	2022-06-30 16:41:50 +02:00
Gwenna Breton	2398110ea5	Added info on dowloading pipelines	2022-06-30 14:24:17 +02:00
Gwenna Breton	22f73b06f9	Updated info about the different profiles	2022-06-30 12:00:05 +02:00
Gwenna Breton	f718025e79	Added doc file for medair	2022-06-30 11:43:04 +02:00
Bruno Grande	6f0d9e6c43	Complete check_max() move to global config	2022-06-23 10:10:28 -07:00
Bruno Grande	1c7230cb08	Add Sage-specific Sarek config	2022-06-23 09:15:42 -07:00
Bruno Grande	2898736cbe	Add Sage Bionetworks nf-core configuration	2022-06-08 14:16:52 -07:00
Åshild J. Vågene	34feaa8b6b	prettier output	2022-06-03 17:08:15 +02:00
Åshild J. Vågene	2d82218318	typo	2022-06-03 16:42:08 +02:00
Åshild J. Vågene	144ca851c1	Update mjolnir_globe.md	2022-06-03 15:36:19 +02:00
Phil Ewels	b51059a3ae	Merge branch 'master' into config_ucph-mjolnir_ash	2022-06-03 13:21:36 +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 A. Fellows Yates	97d57539e3	Apply suggestions from code review ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-03 12:51:20 +02:00
James Fellows Yates	5a67eba04c	Add MAG @ EVA profile	2022-06-03 12:41:08 +02:00
Åshild J. Vågene	1d23ba9264	change name of tmp dir to .tmp_nfcore	2022-06-02 16:40:29 +02:00
Åshild J. Vågene	0f6fb0c10d	Update mjolnir_globe.md	2022-06-02 16:00:22 +02:00