461 commits

Author	SHA1	Message	Date
Kevin Brick	afb6fbb767	Trailing spaces	2021-12-17 00:46:50 -05:00
Kevin Brick	05f7b59573	Update nihbiowulf.md	2021-12-17 00:44:39 -05:00
Kevin Brick	9cf4f69ff3	Add files via upload	2021-12-17 00:37:11 -05:00
praveenraj2018	00a3ed0fa6	Formatting	2021-12-14 21:24:18 +01:00
Praveen	b4d5330c0e	Added rnavar pipeline config for Munin	2021-12-14 03:52:37 +01:00
PCQ	a72f1a243c	Create marvin.md	2021-12-10 17:39:32 +01:00
Venkat Malladi	d722e7206e	Fix readme to remove blob account.	2021-11-18 18:06:54 -06:00
Phil Ewels	4785ceccba	Merge pull request #245 from ikeller/unibe_ibu ... Unibe ibu	2021-11-19 00:56:25 +01:00
Phil Ewels	b25bd1ce42	Update docs/azurebatch.md	2021-11-19 00:54:39 +01:00
Venkat Malladi	ed4c1d5f22	Remove work_dir option.	2021-11-18 17:52:24 -06:00
Phil Ewels	286fa6753a	Apply suggestions from code review	2021-11-19 00:07:33 +01:00
Phil Ewels	a26b3bf1e3	Merge branch 'master' into unibe_ibu	2021-11-19 00:02:30 +01:00
Venkat Malladi	f25dc57f00	Fix headers.	2021-11-18 15:50:12 -06:00
Venkat Malladi	1dacc2f3fe	Fix liniting errors in headers.	2021-11-18 15:49:08 -06:00
Venkat Malladi	845a9ce971	Update Readme with more inforamtion on the options.	2021-11-18 15:47:27 -06:00
Venkat Malladi	219244f1b4	Add in sample datastorage for Illumina Platinum genomes.	2021-11-18 15:28:34 -06:00
Venkat Malladi	237f91a3b7	Add in minmum config for azure.	2021-11-18 14:51:39 -06:00
Harshil Patel	a098ad9e06	Add Chris as main contact at The Crick	2021-11-03 11:11:05 +00:00
Matiss Ozols	5222d7ed9b	added leicester profile	2021-10-21 19:08:06 +01:00
Matiss Ozols	1f58ea42c7	added leicester profile	2021-10-21 19:06:03 +01:00
Matiss Ozols	98a69683c2	added leicester profile	2021-10-21 19:04:48 +01:00
Matiss Ozols	f8b932ae2d	added leicester profile	2021-10-21 18:32:57 +01:00
James A. Fellows Yates	73b6b74c69	Merge pull request #279 from pierrespc/master ... Added Configuration files for running in Maestro HPC at Pasteur Institute, Paris	2021-10-08 19:15:47 +02:00
James A. Fellows Yates	98bbc2b744	Linting	2021-10-08 14:11:39 +02:00
James A. Fellows Yates	b26e495e19	Apply suggestions from code review	2021-10-08 14:08:51 +02:00
pierrespc	2d102eafbc	format docs	2021-10-08 13:46:47 +02:00
pierrespc	035ab61f61	added unlimitedtime profile to maestro; changed cache for bwa process	2021-10-08 09:05:46 +02:00
pierrespc	1621585558	improving documentation	2021-10-04 16:08:33 +02:00
pierrespc	e5d4a357c5	clean doc	2021-10-04 15:08:01 +02:00
pierrespc	136fd44e0c	corrected docs/maestro.config	2021-09-29 13:50:56 +02:00
James A. Fellows Yates	e8b48416bc	Update docs/alice.md	2021-09-28 12:52:31 +02:00
Bjørn Peare Bartholdy	ad83430632	Update docs/alice.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2021-09-28 12:43:54 +02:00
Bjørn Peare Bartholdy	197bd6cfb1	Merge branch 'nf-core:master' into master	2021-09-28 12:09:50 +02:00
bbartholdy	b6ccb46383	add ALICE profile	2021-09-28 12:08:27 +02:00
Mei Wu	c2d74b290a	fix md	2021-09-27 16:25:02 +02:00
Mei Wu	a8a2027f70	Merge branch 'master' into hasta	2021-09-27 16:12:23 +02:00
Mei Wu	ae0adb056f	initial commit	2021-09-27 16:05:19 +02:00
pierrespc	3b593d46ec	merged two pasteur config files for maestro	2021-09-20 15:14:50 +02:00
Harshil Patel	5068e4806f	Merge pull request #271 from theoportlock/master ... Adds Rosalind config for KCL!	2021-09-17 13:36:19 +01:00
theoportlock	0fd5265f7b	Updates the README	2021-09-17 13:21:38 +02:00
pierrespc	b9682bbc91	requires files edited	2021-09-16 12:53:17 +02:00
Marc Trunjer Kusk Nielsen	9a8644ef43	Update computerome.md	2021-09-15 11:10:02 +02:00
Marc Trunjer Kusk Nielsen	cf899a2a4e	Update computerome.md	2021-09-13 08:48:27 +02:00
Marc Trunjer Kusk Nielsen	f46172c25b	Update computerome.md ... Update with usage, heavily inspired by the UPPMAX docs	2021-09-13 08:16:11 +02:00
Marc Trunjer Kusk Nielsen	463df26c72	Merge branch 'nf-core:master' into computerome	2021-09-10 14:47:05 +02:00
theoportlock	b240142cc3	Adds rosalind configuration	2021-09-08 14:33:39 +02:00
Rogan Grant	54298ca0f7	Merge branch 'nf-core:master' into master	2021-09-04 15:37:03 -05:00
Marc Trunjer Kusk Nielsen	aad2486215	Create computerome.md	2021-08-31 14:10:19 +02:00
James Fellows Yates	59af7f0eee	Delete SHH profiles due to decommissioning	2021-08-20 10:15:39 +02:00
Rogan Grant	f793ffaace	Updated iGenomes location	2021-08-03 15:10:54 -05:00
Rogan Grant	079258ebbb	Minor text edits	2021-07-29 11:38:40 -05:00
Rogan Grant	482478878d	Added instructions for module loading	2021-07-28 18:11:10 -05:00
Rogan Grant	40170632aa	First draft of markdown file, with instructions for installing nextflow and getting access	2021-07-28 13:04:32 -05:00
Barry digby	ef6b13e377	tabs rm	2021-07-28 12:19:11 +01:00
Barry digby	f62298d211	w	2021-07-28 11:44:06 +01:00
Barry digby	2fc8082aad	w	2021-07-28 11:43:39 +01:00
Barry digby	11cb6cc70d	w	2021-07-28 11:41:42 +01:00
Barry digby	380adf083a	markdowwwwn	2021-07-28 11:41:16 +01:00
Barry digby	2a06d956b3	mdlint so picky : (	2021-07-27 17:18:42 +01:00
Barry digby	2b6e80561a	Merge branch 'master' of https://github.com/nf-core/configs into	2021-07-27 17:13:17 +01:00
Barry digby	04c0da5a2f	nuig confg (lugh)	2021-07-27 17:05:27 +01:00
ameynert	5c56e13747	Fix typo	2021-07-23 10:18:02 +01:00
ameynert	3bfaf65450	Fixed trailing space	2021-07-23 09:39:32 +01:00
ameynert	26183d9883	Updated eddie documentation for singularity cache directory	2021-07-23 09:35:15 +01:00
ameynert	5224eb5574	Updated resources folder & institute name ... Local resources folder was re-organized & re-named BioinformaticsResources. Added note about viralrecon & atacseq pipeline-specific config. IGMM name-changed recently; updated to IGC.	2021-07-21 12:15:17 +01:00
Maxime U. Garcia	30e058abf0	Merge branch 'master' into master_kraken	2021-07-20 09:26:56 +02:00
Gisela Gabernet	e2088a008d	Merge branch 'master' into master	2021-07-03 12:24:42 +02:00
ggabernet	ee2e8392ab	add aws_tower profile	2021-07-03 12:17:21 +02:00
Edmund Miller	21e1037e0c	docs(sysbio): Add rnaseq specific docs	2021-06-17 09:18:45 -05:00
Edmund Miller	41ae99d34a	feat(sysbio): Add cleanup	2021-06-17 08:17:55 -05:00
Edmund Miller	87c8e346e0	fix(sysbio): Change filetype	2021-06-17 08:14:48 -05:00
Edmund Miller	2a958f5ce3	docs: Add sysbio	2021-06-16 21:19:38 -05:00
ikeller	af1e57027d	edit config and readme	2021-05-19 09:46:07 +02:00
Barry digby	24a4119e43	memory test	2021-04-29 14:24:57 +01:00
Barry digby	8340e89768	nuig.config first commit	2021-04-28 17:28:01 +01:00
Alexander Peltzer	c12c373969	Merge pull request #235 from aunderwo/cambridge ... Add Cambridge University HPC config	2021-04-25 10:40:56 +02:00
Anthony Underwood	982d1a8f2a	Fix markdown linting	2021-04-22 16:41:05 +01:00
Anthony Underwood	29dcc160e3	Create cambridge.md	2021-04-22 16:04:29 +01:00
Anthony Underwood	3e8f9b3d4e	Remove blank lines	2021-04-22 15:57:09 +01:00
Anthony Underwood	f414446a88	Add info on how to load Singularity into your path	2021-04-22 15:38:36 +01:00
Anthony Underwood	b16b011bcc	Add ~/bin as recommended location for nextflow executable	2021-04-22 12:02:11 +01:00
Anthony Underwood	cc18d213dc	Update sanger.md	2021-04-21 20:24:08 +01:00
Anthony Underwood	40eb3e0201	Update sanger.md	2021-04-21 20:20:30 +01:00
Anthony Underwood	7163e8723d	Create sanger.md	2021-04-21 20:17:42 +01:00
Maxime Garcia	1548690ca6	Update docs/uppmax.md ... Co-authored-by: Pontus Freyhult <pontus_github@soua.net>	2021-04-21 12:27:27 +02:00
MaxUlysse	bab9241243	fix: markdownlint	2021-04-21 11:51:14 +02:00
MaxUlysse	844246cc7d	fix: clearer usage of module	2021-04-21 11:28:58 +02:00
MaxUlysse	1a7ec56c33	feat: more details	2021-04-21 11:23:50 +02:00
MaxUlysse	c89877decc	feat: use <PIPLEINE>	2021-04-21 11:17:06 +02:00
MaxUlysse	658fa7ccda	fix: markdownlint	2021-04-21 11:08:16 +02:00
Maxime Garcia	79e3dd65a7	Apply suggestions from code review ... Co-authored-by: Pontus Freyhult <pontus_github@soua.net>	2021-04-21 11:06:39 +02:00
Maxime Garcia	4eea06f0db	Apply suggestions from code review ... Co-authored-by: Pontus Freyhult <pontus_github@soua.net>	2021-04-20 16:03:34 +02:00
MaxUlysse	1c1dd952fc	fix: bullet list	2021-04-20 15:58:51 +02:00
Maxime Garcia	e4d2ef0984	Apply suggestions from code review ... Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>	2021-04-20 15:53:54 +02:00
MaxUlysse	4930795cab	feat: more complete docs	2021-04-20 15:38:49 +02:00
MaxUlysse	10abca712b	fix: first draft of bianca guide	2021-04-16 17:01:58 +02:00
James A. Fellows Yates	12a4518803	Markdown lint fix	2021-04-15 22:29:15 +02:00
James A. Fellows Yates	0fc90586e0	Update mpcdf.md	2021-04-15 22:26:37 +02:00
MaxUlysse	3918e0aa9d	feat: remove kraken profile	2021-04-13 15:14:14 +02:00
James A. Fellows Yates	161c3a33d4	Merge branch 'master' into eva	2021-04-07 19:28:16 +02:00
Alexander Peltzer	91f50aad4e	Merge pull request #221 from phue/biohpc_gen ... Add BioHPC Genomics config	2021-04-07 14:03:22 +02:00
James Fellows Yates	8dac4ca552	Merge branch 'eva' of github.com:jfy133/configs into eva	2021-04-06 17:53:32 +02:00
James Fellows Yates	60c66d93ac	Markdown linting	2021-04-06 17:53:27 +02:00
James A. Fellows Yates	832edaa450	Merge branch 'master' into eva	2021-04-06 17:51:46 +02:00
James Fellows Yates	be1d35840d	Add EVA and EAGER@EVA	2021-04-06 17:48:16 +02:00
ameynert	700776f759	Change to shared Singularity cache	2021-03-30 16:11:15 +01:00
phue	7c5a0871a3	add note about required nextflow version	2021-03-29 19:36:49 +02:00
phue	8fc60e2e70	add config for biohpc_gen	2021-03-29 19:25:58 +02:00
Gisela Gabernet	71a97ba316	Merge pull request #185 from ggabernet/master ... awsbatch config update	2021-03-28 20:59:40 +02:00
ameynert	3a8e54f153	Removed sneaky trailing whitespace.	2021-03-24 13:58:10 +00:00
ameynert	a0d42f5153	Fixed code blocks for markdown linting	2021-03-24 13:55:31 +00:00
Phil Ewels	bfab371c94	Merge branch 'master' into master	2021-03-24 12:36:15 +01:00
ameynert	2a8ae2b214	Update eddie.md	2021-03-24 11:12:41 +00:00
ameynert	96fe6185a0	IGMM-specific docs	2021-03-24 11:01:41 +00:00
Asaf Peer	9b2d5bfead	Merge pull request #216 from asafpr/master ... Added JAX conf	2021-03-24 03:31:14 -04:00
ameynert	791f3c95f3	Pipeline specific configs moving to confs/pipeline	2021-03-23 16:07:07 +00:00
Alexander Peltzer	5988c51361	Merge pull request #211 from DoaneAS/master ... Adding WCM.config for Weill Cornell Medicine cluster	2021-03-23 14:58:27 +01:00
Asaf Peer	30c864e112	added JAX conf	2021-03-21 06:49:11 -04:00
ameynert	b48136a62e	Added pipeline-specific config files	2021-03-18 12:55:03 +00:00
ameynert	af6a6b1060	Details on running on eddie ... Removed Conda support, Singularity by default. Added login and screen session on wild west node options.	2021-03-18 12:48:48 +00:00
ameynert	4ad6bb2bec	Singularity info	2021-03-17 14:50:40 +00:00
Noirot Céline	e3216ccf79	typo	2021-03-16 16:00:56 +01:00
Noirot Céline	cc17045914	Add institution	2021-03-16 15:58:29 +01:00
Noirot Céline	7e9f83ee81	Add IFB config	2021-03-16 15:54:19 +01:00
Ashley S Doane	6343a7f87c	Update wcm.md	2021-03-11 14:01:07 -05:00
Ashley S Doane	d630bcfb6c	Create wcm.md	2021-03-11 13:59:55 -05:00
ameynert	4c0111f598	Eddie profile documentation initial commit	2021-03-04 14:46:58 +00:00
James A. Fellows Yates	0bac3691e3	Create mpcdf.config	2021-02-14 18:07:40 +01:00
James Fellows Yates	a78aac327d	Linting fixes	2021-02-14 17:58:50 +01:00
James Fellows Yates	537f52a640	Add MPI-EVA profile	2021-02-14 17:50:20 +01:00
ggabernet	0909708b97	update with upstream	2021-02-09 22:01:27 +01:00
Charles Plessy	1608b36dcf	Institutional profile for Okinawa Institute of Science and Technology	2021-02-02 17:40:10 +09:00
James A. Fellows Yates	c4604450d8	Update seg_globe.md	2021-01-21 13:04:12 +01:00
Åshild J. Vågene	bcd137225e	Update and rename ceh.md to seg_globe.md	2021-01-21 11:46:46 +01:00
Åshild J. Vågene	ef80452577	Update docs/ceh.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2021-01-21 11:16:46 +01:00
James A. Fellows Yates	2fd475c339	Fix some linting errors	2021-01-21 06:30:43 +01:00
Åshild J. Vågene	d108666950	Update ceh.md	2021-01-21 00:30:54 +01:00
Åshild J. Vågene	65831b73ef	Create ceh.md	2021-01-21 00:17:08 +01:00
Combiz Khozoie	a61992d144	Added institutional configs for Imperial and Imperial MEDBIO. Added institutional pipeline configs for scflow for Imperial and Imperial MEDBIO	2020-12-18 10:21:26 +00:00
arontommi	ac108379cd	trailing spaces	2020-11-26 13:58:16 +01:00
arontommi	c2c7265518	fix linting errors	2020-11-26 13:47:47 +01:00
arontommi	6480aef1db	typo	2020-11-26 11:41:33 +01:00
arontommi	f84fbb8f89	typo	2020-11-26 11:39:51 +01:00
arontommi	e6bb7a4852	capital names	2020-11-26 11:37:59 +01:00
arontommi	5726ef3456	typo	2020-11-26 11:26:08 +01:00
arontommi	06469901fe	typo	2020-11-26 11:24:29 +01:00
arontommi	ebf754bf43	documentation for bianca	2020-11-26 09:53:51 +01:00
Phil Ewels	e96455e180	Update docs/uppmax.md	2020-11-26 01:43:09 +01:00
Phil Ewels	d9a8009662	Better UPPMAX docs	2020-11-25 22:45:16 +01:00
Andrew Frank	d70fc2605a	Fix parameters in google.md ... Change parameters from hyphens to underscores to accurately reflect google.config	2020-11-12 11:52:58 -05:00
Gisela Gabernet Garriga	885f0ce5f6	awsbatch config update	2020-11-09 22:41:38 +01:00
lecorguille	e3d733d87e	Add ABiMS - fix lint	2020-10-23 09:29:54 +02:00
lecorguille	4d03f72c78	Add ABiMS - last bits of doc	2020-10-23 09:27:12 +02:00
lecorguille	6ee6b7bf56	Add ABiMS - remove a useless link	2020-10-23 00:12:02 +02:00
lecorguille	23ba1c58b1	Add ABiMS - NXF_SINGULARITY_CACHEDIR	2020-10-23 00:11:58 +02:00
lecorguille	f21d16b24f	Add ABiMS - fix lint	2020-10-22 17:47:25 +02:00
lecorguille	a63ca751ee	Add ABiMS	2020-10-22 16:57:41 +02:00
James A. Fellows Yates	7088ed196f	Update mpcdf.md	2020-10-22 11:08:29 +02:00
James A. Fellows Yates	0d6e269322	Update mpcdf.md	2020-10-15 14:24:08 +02:00
James A. Fellows Yates	9df85be081	Update mpcdf.md	2020-09-03 20:27:15 +02:00
James A. Fellows Yates	09cd5cad65	Update mpcdf.md	2020-09-03 20:25:37 +02:00
James A. Fellows Yates	0501ae4c1a	Started docs for mpcdf	2020-09-03 20:21:49 +02:00
James A. Fellows Yates	09cfabd37f	Add new microbiome_screening profile to docs	2020-08-11 09:20:31 +02:00
drpatelh	165af5122f	Update docs	2020-08-03 11:39:23 +01:00
jfy133	15dad7e2e7	Add caveats for EAGER @ SHH profiles	2020-07-08 09:47:03 +02:00
James A. Fellows Yates	b2e043ab59	Add documentation for HOPS profile for eager @ SHH	2020-07-07 14:35:42 +02:00
Phil Ewels	cd9fbb22dc	Merge pull request #161 from ewels/uct_hpc ... Update UCT hex -> hpc	2020-06-22 09:18:43 +02:00
Phil Ewels	29f5fa6ce4	uct_hpc docs, readme	2020-06-17 15:22:42 +02:00
Phil Ewels	17824d2d62	Merge czbiohub_aws_highpriority profile into czbiohub_aws	2020-06-16 15:20:39 +02:00
phue	6d356cc918	CBE: don't load singularity module ... singularity is now installed from CentOS repos, the environment module will be removed	2020-06-05 12:07:26 +02:00
Alexander Peltzer	f877644059	Merge branch 'master' into master	2020-05-29 11:43:47 +02:00
Alexander Peltzer	dd56355c7c	Update bi.md ... No trailing spaces it said.	2020-05-28 10:18:16 +02:00
Alexander Peltzer	f4df5b5a75	Add BI Docs	2020-05-28 10:16:22 +02:00
Alexander Peltzer	6011419454	Merge pull request #154 from jfy133/master ... Update SHH nf-core/eager group-specific profiles	2020-05-27 17:52:09 +02:00
James A. Fellows Yates	0943ba088a	Mention SHH EAGER group-specific profiles	2020-05-26 11:14:42 +02:00
James A. Fellows Yates	2e3b577fb3	Typo fixes ... I'll never forgive our directory for that name...	2020-05-07 11:50:11 +02:00
James A. Fellows Yates	38e9e54932	Merge pull request #151 from jfy133/master ... Add additional custom nf-core/eager params for SHH profile	2020-05-07 09:25:02 +02:00
James A. Fellows Yates	0a312cd2c9	Update shh.md	2020-05-07 09:17:56 +02:00
James A. Fellows Yates	4804052b23	Update SHH nf-core/eager pipeline docs	2020-05-04 21:04:17 +02:00
MaxUlysse	e6f4d58fa6	update rnafusion munin specific config	2020-04-28 17:06:04 +02:00
Adrian	1e68a10ef0	adding documentation for icr_davros	2020-04-28 16:02:26 +01:00
MaxUlysse	50a44d037b	better docs and organisation of giles	2020-04-09 17:02:36 +02:00
Daniel Lundin	c8de9be701	Adding UPPMAX specific config for ampliseq	2020-03-31 15:17:24 +02:00
MaxUlysse	d4bea56f52	add munin/rnafusion specific docs + markdownlint	2020-03-11 14:23:23 +01:00
MaxUlysse	7c60096952	update docs for munin/sarek specific config	2020-03-11 14:17:24 +01:00
MaxUlysse	250035e71d	fix path to config files	2020-03-11 14:11:23 +01:00
Edmund Miller	1c62395332	docs(utd_ganymede): add initial documentation	2020-03-09 20:07:46 -05:00
James A. Fellows Yates	52214cc22d	Merge pull request #134 from marcel-keller/ebc ... adding Estonian Biocentre cluster profile	2020-03-09 16:09:27 +01:00
marcel-keller	dcb478c904	Update ebc.md	2020-03-09 17:07:03 +02:00
marcel-keller	88cfe11187	Update ebc.md	2020-03-09 16:32:14 +02:00
marcel-keller	418f4b52b6	Create ebc.md	2020-03-09 16:23:16 +02:00
Alexander Peltzer	b8d020b78c	Update cfc.md	2020-03-09 15:12:49 +01:00
Evan Floden	6141e008a3	Update google.md	2020-03-09 14:44:58 +01:00
Evan Floden	d8ad376f71	Merge branch 'master' into master	2020-03-06 10:29:50 +00:00
Evan Floden	f5364e45e7	Update google.md or markdown linting	2020-03-06 11:27:44 +01:00
Alexander Peltzer	59a787b179	Merge pull request #122 from marchoeppner/ccga-config ... Removing old CCGA profile from docs and linting	2020-03-06 11:17:08 +01:00
mseybold	2135996b13	Update cfc.md	2020-03-06 11:12:21 +01:00
Evan Floden	87e8da61a4	Readme formatting	2020-03-06 05:58:59 +00:00
Evan Floden	8a9d3ad8a0	First commit of Google Cloud config	2020-03-06 05:47:29 +00:00
Marc Hoeppner	6c5a5c8bcb	Removing old CCGA profile from docs and linting ... Removing CCGA profile from master config Removing CCGA profile from master config	2020-02-24 12:16:33 +01:00