382 commits

Author	SHA1	Message	Date
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
Maxime Garcia	08e2804b37	Merge branch 'master' into Uppmax	2020-02-20 17:18:46 +01:00
MaxUlysse	aa905cd645	add UPPMAX specific sarek config	2020-02-20 17:14:18 +01:00
marchoeppner	0830203b70	Adding new CCGA Med Cluster to profiles ... Updating README and fixing linting errors in CCGA_MED profile Fixing order in profile queue and removed leading slash from readme for ccga profile docs Fixing order in profile queue and removed leading slash from readme for ccga profile docs	2020-02-11 11:12:51 +01:00
James A. Fellows Yates	799f2d5788	Grammar tweak	2019-12-21 20:59:48 +01:00
James A. Fellows Yates	435a5892ea	Updated docs corresponding to 638758423a	2019-12-21 20:59:25 +01:00
drpatelh	bcb8950c2f	Change URL to website	2019-12-18 10:57:12 +00:00
drpatelh	be5ed21269	Update docs	2019-12-18 10:54:31 +00:00
drpatelh	0779d25255	Update docs	2019-12-12 13:02:51 +00:00
Alexander Peltzer	a6d08ed646	Adjust custom pipeline config for ampliseq on BINAC	2019-12-11 16:09:44 +01:00
Maxime Garcia	9497b78149	Merge pull request #100 from MaxUlysse/UPPMAX ... Improve UPPMAX configs	2019-12-06 10:52:44 +01:00
Maxime Garcia	79528de92f	Update docs/uppmax.md ... Co-Authored-By: Phil Ewels <phil.ewels@scilifelab.se>	2019-12-06 10:47:09 +01:00
jfy133	1650080b6e	Linting	2019-12-05 17:03:07 +01:00
jfy133	731372dac2	Added SHH specific EAGER configuration	2019-12-05 17:01:10 +01:00
MaxUlysse	a63ec24626	Merge branch 'UPPMAX' of github.com:MaxUlysse/nf-core_configs into UPPMAX	2019-12-05 15:18:04 +01:00
MaxUlysse	99afe86ea9	update docs	2019-12-05 15:18:01 +01:00
Maxime Garcia	78826c9d4e	Merge branch 'master' into UPPMAX	2019-12-05 12:52:34 +01:00
Alexander Peltzer	9cdb915efb	Merge pull request #101 from jfy133/master ... Condensing SHH profile(s) with sub-profiles	2019-12-05 12:51:31 +01:00
jfy133	54dafbcfa3	Condensing SHH profiles following https://github.com/nf-core/configs/pull/100	2019-12-05 12:09:11 +01:00
MaxUlysse	cdbdbee0eb	replace -profile uppmax_devel by -profile uppmax,devel	2019-12-05 11:49:44 +01:00
Maxime Garcia	2669401a72	Merge branch 'master' into sarek	2019-11-27 13:27:43 +01:00
James A. Fellows Yates	c725c71e4d	Merge branch 'master' into master	2019-11-26 20:34:42 +01:00
jfy133	6f40c13473	Split shh config for each cluster	2019-11-26 20:20:17 +01:00
phue	672f025639	cbe: add documentation about iGenomes	2019-11-26 18:09:20 +01:00
Alexander Peltzer	81739a3907	Merge pull request #93 from jfy133/master ... Updated max resources for SHH SDAG	2019-11-26 15:56:39 +01:00
James A. Fellows Yates	89506a653c	Remove empty lines in block quotes for linting	2019-11-26 15:34:25 +01:00
James A. Fellows Yates	12ec22838c	Specified max sources currently at SDAG limits (exceeds cdag)	2019-11-26 15:29:03 +01:00
noirot	07b1f17d6a	correct md to pass linter	2019-11-26 15:02:06 +01:00
Noirot Céline	3ed206b7a7	Update docs/genotoul.md ... ok Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>	2019-11-26 14:52:45 +01:00
Noirot Céline	288294994e	Update docs/genotoul.md ... ok Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>	2019-11-26 14:52:32 +01:00
noirot	e95196451f	correct md to pass linter	2019-11-26 14:47:23 +01:00
noirot	42c949db95	correct md to pass linter	2019-11-26 14:43:42 +01:00
Alexander Peltzer	23f9fd2d73	Merge branch 'master' into master	2019-11-26 14:20:36 +01:00
Noirot Céline	42d99e7006	Update genotoul.md	2019-11-26 13:18:34 +01:00
Maxime Garcia	f6c2e4c65f	Update docs/pipeline/sarek/munin.md ... Update conf/pipeline/sarek/munin.config testing out module and containers collision	2019-11-26 11:57:51 +01:00
MaxUlysse	25d4e92935	update docs	2019-11-26 11:55:36 +01:00
Maxime Garcia	b029ccaa59	Update docs/pipeline/sarek/munin.md ... Update conf/pipeline/sarek/munin.config	2019-11-26 11:48:11 +01:00
MaxUlysse	283abcece4	update docs	2019-11-26 11:25:29 +01:00
MaxUlysse	cd1d0b5f8f	Add specific sarek config base, munin specific sarek config and docs ... rename file improve configs remove unnecessary params	2019-11-26 11:25:29 +01:00
Alexander Peltzer	aeb2fb6dc0	Fix all the markdownlinting errors	2019-11-26 00:48:17 +01:00
Noirot Céline	ed4436c1a6	Merge branch 'master' into master	2019-11-25 16:24:12 +01:00
noirot	db51c49b2f	Add genotoul config	2019-11-25 14:54:25 +01:00
MaxUlysse	08a6b74825	add new profile to be shared: awsbatch	2019-11-19 14:16:06 +01:00
Alexander Peltzer	d2603a134e	Add in denbi cloud configs	2019-11-11 12:26:19 +01:00
Phil Ewels	6790dbd4a3	Merge pull request #82 from arontommi/dev ... documentation on how to fix bianca "Requested node configuration is not available" problem	2019-11-08 15:07:07 +01:00
Phil Ewels	5e7d13df89	Update uppmax.md	2019-11-08 10:59:34 +01:00
arontommi	3f534c154e	documentation on how to fix bianca cluster configuration problem	2019-11-07 13:06:31 +01:00
arontommi	99f4d9b9bd	documentation on how to fix bianca cluster configuration problem	2019-11-06 13:10:09 +01:00
maxibor	47a7d57db4	update shh doc	2019-10-28 16:09:00 +01:00
phue	5a9dbe5d7c	MENDEL is no more ... the cluster is no longer operational, was replaced by CBE	2019-10-28 14:11:34 +01:00
Alexander Peltzer	5348b8c609	Revert "BINAC SMP / Short / Long Updates"	2019-10-28 13:12:31 +01:00
Alexander Peltzer	b5b2dd817f	Merge all	2019-10-27 13:24:45 +01:00
Anthony Bretaudeau	883a761651	add link	2019-10-16 18:45:26 +02:00
Anthony Bretaudeau	1f2786c78f	add genouest cluster	2019-10-16 18:15:04 +02:00
phue	9b3fda36f6	update singularity version ... singularity/3.1.0 is not available anymore	2019-10-10 21:22:19 +02:00
phue	5e257e7e9a	add cbe profile	2019-09-22 16:45:09 +02:00
MaxUlysse	f69524d59a	feat: update docs	2019-08-07 11:56:10 +02:00
MaxUlysse	332ba0dadb	fix: update and rearrange munin configuration file and docs	2019-08-07 11:10:48 +02:00
Martin Proks	c583aa0233	Added kraken config (#15) ... * Added kraken template * docs: updated some info * fix: updated igenomes_base path	2019-08-05 11:19:05 +02:00
Alexander Peltzer	82ffedf895	Drop aquila	2019-07-30 18:53:36 +02:00
Alexander Peltzer	4e48d4cc62	Fix remaining points by drpatelh	2019-07-30 18:53:00 +02:00
Alexander Peltzer	35c715ca3b	Merge remote-tracking branch 'upstream/master'	2019-07-30 16:53:19 +02:00
Remi Planel	1c0d596582	Merge remote-tracking branch 'upstream/master'	2019-07-30 16:15:20 +02:00
Remi Planel	be28a34839	Updat Pasteur doc	2019-07-30 16:12:30 +02:00
Remi Planel	64e78a3dc1	Update the doc	2019-07-30 15:17:25 +02:00
Remi Planel	6f264ac2ca	Add pasteur profile doc	2019-07-30 15:15:30 +02:00
marchoeppner	b74f020f14	Update docs/ccga_dx.md ... Co-Authored-By: Harshil Patel <drpatelh@users.noreply.github.com>	2019-07-29 12:45:30 +02:00
marchoeppner	71bc98afae	Adding config file for CCGA dx cluster	2019-07-29 12:06:29 +02:00
Olga Botvinnik	474e98daaf	Merge branch 'master' into olgabot/czb-update	2019-07-09 16:02:25 -07:00
marchoeppner	fe0153befd	Updating CCGA documentation	2019-07-05 08:30:02 +02:00
marchoeppner	d66bf4e478	Updating CCGA documentation	2019-07-05 08:28:18 +02:00
Olga Botvinnik	b82d68c009	Add docs	2019-06-24 17:55:01 -07:00
Alexander Peltzer	ebe838ac7e	Merge pull request #45 from czbiohub/olgabot/czbiohub ... [WIP] Add CZ Biohub	2019-06-06 13:35:34 +02:00
Olga Botvinnik	ad7e26ea69	Write out docs for czbiohub" ... git push	2019-06-05 14:42:24 -07:00
Alexander Peltzer	515e9484de	Merge pull request #44 from drpatelh/dev ... Add proper nf-core logo	2019-06-01 12:36:57 +02:00
drpatelh	ac804859f4	Add nf-core logo	2019-05-31 00:47:06 +01:00
Alexander Peltzer	0acdcc3813	Add Aquila Config Singapore	2019-05-04 23:20:15 +02:00
Tobias Schraink	d91b06d884	added missing line in prince and bigpurple docs	2019-04-18 14:25:27 -04:00
Tobias Schraink	4ba831705d	added nyu prince and bigpurple md files, added singularity cacheDir to prince and bigpurple configs	2019-04-18 14:13:02 -04:00
KochTobi	aaa7be049a	Update cfc config ... * Change singularity version documentation	2019-03-16 14:11:59 +01:00