455 commits

Author	SHA1	Message	Date
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
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
qlr900	7d59eabd91	simplify guideline	2022-07-06 09:52:06 +02:00
qlr900	941a34406a	update ku_sund_dangpu.md	2022-07-05 12:06:19 +02:00
qlr900	8ba35f721c	add ku_sund_dangpu.md	2022-07-05 12:05:10 +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
nf-core-bot	28c3cca5e7	[automated] Fix linting with Prettier	2022-06-07 10:03:04 +00:00
Maxime U. Garcia	3eca377514	Merge branch 'master' into gis-branch	2022-06-07 11:58:20 +02:00
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
Phil Ewels	b38a0077c2	Merge branch 'master' into gis-branch	2022-06-03 13:20:45 +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
Åshild J. Vågene	e871dc87f9	Update mjolnir_globe.md	2022-06-02 15:59:11 +02:00
Åshild J. Vågene	940077190b	Update mjolnir_globe.md	2022-06-02 15:38:40 +02:00
Åshild J. Vågene	2988e33576	Create mjolnir_globe.md	2022-06-02 15:38:07 +02:00
Nicolas Vannieuwkerke	867dcabd97	Fix type in VSC UGent	2022-05-20 10:36:07 +02:00
Nicolas Vannieuwkerke	8432e4d1dc	typo	2022-05-20 09:49:42 +02:00
Nicolas Vannieuwkerke	fa39478a2d	prettier	2022-05-20 09:49:04 +02:00
Nicolas Vannieuwkerke	c2b26a734d	automated the internal cache dir location for singularity	2022-05-20 09:48:19 +02:00
nvnieuwk	b2f7538b33	Update docs/vsc_ugent.md ... Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>	2022-05-20 09:42:31 +02:00
nvnieuwk	a3583262c2	Update docs/vsc_ugent.md ... Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>	2022-05-20 09:41:02 +02:00
nvnieuwk	dba85e53fa	Update docs/vsc_ugent.md ... Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>	2022-05-20 09:40:55 +02:00
Nicolas Vannieuwkerke	a2d77df2ee	added default scratch location to markdown file	2022-05-20 09:32:14 +02:00
Nicolas Vannieuwkerke	2f74c91145	prettier	2022-05-20 09:18:33 +02:00
Nicolas Vannieuwkerke	cc86e6b270	Added the VSC UGent profile	2022-05-20 09:12:18 +02:00
Sarah Guinchard	be9711731a	Merge pull request #375 from nf-core/ifb_core-config-update ... Ifb core config update	2022-05-13 14:45:44 +02:00
sofstam	ca4cdcffee	Fix typo	2022-05-12 15:07:30 +02:00
Sarah Guinchard	84457cc655	Update documentation	2022-05-12 11:01:36 +02:00
sofstam	c59149d64c	Update docs for hasta config	2022-05-12 10:47:03 +02:00
James Fellows Yates	e1f780d976	Add taxprofiler for eVA	2022-05-12 07:54:17 +01:00
James Fellows Yates	4885b672b1	Prettier	2022-04-25 11:46:32 +02:00
Alex Rajewski	766eb450be	usage notes	2022-04-22 10:23:19 -07:00
James A. Fellows Yates	b0c9ac9be8	Update eva.md	2022-03-28 09:02:26 +02:00
b97pla	9a6cdfc21e	removed process-specific requirements for sarek, request miarka high-mem node	2022-03-24 14:25:43 +01:00
b97pla	5466d927f1	added requirements for uppmax cluster miarka	2022-03-23 15:29:40 +01:00
Edmund Miller	6c37bf3b20	style: Run prettier	2022-03-21 19:23:28 -05:00
James A. Fellows Yates	962d86d604	Merge pull request #346 from sagc-bioinformatics/sahmri ... Added SAHMRI profile	2022-03-18 13:01:36 +01:00
ajodeh-juma	188c3a39cc	add gis.md documentation	2022-03-16 16:17:54 +03:00
ajodeh-juma	06854c9f2d	add gis.md documentation	2022-03-16 15:34:36 +03:00
James A. Fellows Yates	a2e2e94333	Merge pull request #344 from njspix/vai ... Add VAI configuration	2022-03-14 14:36:00 +01:00
Nathan Watson-Haigh	dba3fb4c1d	Added SAHMRI HPC profile docs	2022-03-13 00:05:34 +10:30
Nathan Watson-Haigh	b638694bd0	Added SAHMRI HPC profile	2022-03-12 21:17:33 +10:30
Matiss	6c79c75eec	Merge pull request #290 from maxozo/master ... added leicester profile	2022-03-11 09:21:09 +00:00
Spix	429c7b4fa8	initial commit	2022-03-07 15:01:46 -05:00
Alexander Peltzer	d0d86bfb2a	Merge pull request #339 from jfy133/rnaseq_mpcdf ... Add RNASEQ specific config for MPCDF	2022-03-07 13:59:08 +01:00
James A. Fellows Yates	975fca6721	Apply suggestions from code review	2022-03-07 13:51:00 +01:00
Natalia Zajac	c2e0c9e6d4	Update on md file	2022-03-07 12:59:56 +01:00
Natalia Zajac	e07a0e548e	Config Addition	2022-03-04 12:16:01 +01:00
James Fellows Yates	70318c3b2a	Tweak eager settigs	2022-03-03 14:29:30 +01:00
James Fellows Yates	7112e74b73	Tweak settings based on latest batch specs	2022-03-03 13:43:40 +01:00
James Fellows Yates	e649bfbb2e	Linting	2022-03-03 12:26:14 +01:00
James Fellows Yates	94f8cbcb84	Add rnaseq pipeline specific config for MPCDF	2022-03-03 12:20:02 +01:00
James A. Fellows Yates	121452afad	Linting	2022-03-02 08:51:20 +01:00
James A. Fellows Yates	15a0571eae	Fix markdown	2022-03-02 08:50:42 +01:00
James A. Fellows Yates	adcfe22f98	Remove draco entry to MPCDF profiles due to decomissioning	2022-03-02 08:38:55 +01:00
James A. Fellows Yates	a6c12d8edc	Merge pull request #322 from U-BDS/master ... Add UAB Cheaha profile	2022-03-01 08:29:54 +01:00
James A. Fellows Yates	4fbebac9b3	Merge pull request #304 from PCQuilis/patch-1 ... Create marvin.md added marvin config	2022-02-28 15:03:07 +01:00
James A. Fellows Yates	d6f5209afc	Update marvin.md	2022-02-28 15:01:12 +01:00
Combiz Khozoie	a77f718ae2	Merge pull request #330 from nf-core/master ... Pulling master to branch	2022-02-11 14:18:01 +00:00
Matthias Hörtenhuber	b98ab26662	fix markdownlint errors	2022-02-11 14:09:16 +01:00
Combiz Khozoie	34d9e7a967	Update imperial.md ... Updated docs to reflect use of internal profiles	2022-02-11 00:08:08 +00:00
Combiz Khozoie	5aa1abda26	Delete imperial_mb.md ... Deprecated in favour of internal profiles within the single imperial.config	2022-02-11 00:07:05 +00:00
Combiz Khozoie	14c7662762	Update imperial.md ... Updated docs to reflect restructuring for internal profiles	2022-02-10 23:49:43 +00:00
phue	a6dd3aa0f1	cbe: update recommended nextflow version in docs ... otherwise, the new anaconda requirements will cause conflicts	2022-02-04 10:21:52 +01:00
Lara Ianov	f876227a38	added note on screen, conda, and interactive partitions	2022-01-28 12:18:11 -06:00
Austyn Trull	06541411dd	Initial commit of cheaha profile	2022-01-28 11:37:42 -06:00
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