774 commits

Author	SHA1	Message	Date
James A. Fellows Yates	f725b6c431	Apply suggestions from code review	2022-03-15 07:36:34 +01:00
Nathan S. Watson-Haigh	a0f5ac7445	Added references subdir to igenomes_base	2022-03-15 11:41:51 +10:30
James A. Fellows Yates	4670f8bf0c	Update eva.config	2022-03-14 14:56:01 +01:00
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	cc55026751	Add singularity to PATH	2022-03-13 07:39:31 +10:30
Nathan Watson-Haigh	2f0b022571	Fixed typos	2022-03-13 00:08:42 +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
Nathan Spix	d067f61329	remove extra spaces	2022-03-07 15:22:18 -05:00
Spix	17c77ad516	update singularity command	2022-03-07 15:13:26 -05:00
Spix	c97c48ae5b	update singularity command	2022-03-07 15:11:45 -05:00
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	97058995ef	Update on singularity cache	2022-03-07 12:37:01 +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 A. Fellows Yates	546393ed18	Apply suggestions from code review	2022-03-03 14:22:35 +01:00
ilight1542	5a0543e4ac	Merge branch 'rnaseq_mpcdf' into mpcdf_eager_config_update	2022-03-03 14:17:18 +01:00
ilight1542	25c644abb7	modified mpcdf configs (general + eager)	2022-03-03 13:55:02 +01:00
James Fellows Yates	7112e74b73	Tweak settings based on latest batch specs	2022-03-03 13:43:40 +01:00
James A. Fellows Yates	17312604cf	Update mpcdf.config	2022-03-03 12:25:06 +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	5547e45ab5	Merge branch 'master' into jfy133-patch	2022-03-02 08:28:22 +01:00
James A. Fellows Yates	ea052a7b67	Merge pull request #334 from jfy133/eva-update ... eva: generalise custom SGE mem flag	2022-03-01 09:23:04 +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
PCQ	1ff92db608	Merge branch 'nf-core:master' into master	2022-02-28 14:50:41 +01:00
James A. Fellows Yates	89f6484325	Merge pull request #319 from maltesemike/patch-2 ... Update mpcdf.config	2022-02-28 14:06:06 +01:00
James A. Fellows Yates	46f046d477	Update eva.config	2022-02-28 14:00:37 +01:00
James A. Fellows Yates	d7d9951dbf	Insert h_vmem for all nf-core pipelines	2022-02-28 14:00:16 +01:00
James A. Fellows Yates	6210ee874c	Update eva.config	2022-02-28 13:57:37 +01:00
Mei Wu	dcba537d15	picard md is single threaded	2022-02-21 16:19:17 +01:00
Maxime U. Garcia	41e00ae8f9	Update conf/munin.config	2022-02-14 13:11:46 +01:00
Praveen Raj S	90936a5518	Added: runOptions to singularity ... To bind external mount directories at runtime.	2022-02-14 12:45:20 +01:00
Combiz Khozoie	2d434c6ee5	Merge pull request #321 from nf-core/combiz-patch-1 ... Imperial config updates	2022-02-11 14:49:30 +00:00
Maxime U. Garcia	4a936a685e	Merge pull request #317 from nf-core/praveenraj2018-patch-1 ... Added genome parameter	2022-02-11 15:33:18 +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
Combiz Khozoie	3ce32f50c4	Update imperial.config ... Moved params configs from internal profile to universal	2022-02-11 11:02:40 +00:00
Combiz Khozoie	b99b74b2d3	Update imperial.config ... Fixed indent	2022-02-11 00:26:45 +00:00
Combiz Khozoie	38a05a6531	Update imperial.config ... Reworked to use internal profiles for the Imperial HPC and the MedBio cluster.	2022-02-10 23:46:14 +00:00
Combiz Khozoie	e1d0bf0cd2	Delete imperial_mb.config ... Separate config for the medbio queue now deprecated in favour of an internal profile within the main imperial.config	2022-02-10 23:44:49 +00:00
Combiz Khozoie	fe5474a029	Update imperial.config ... Multiple process level updates reflecting the latest job sizing guidelines for the Imperial HPC	2022-02-10 23:02:47 +00:00
Harshil Patel	8fa6ab9b35	Merge pull request #323 from stevin-wilson/patch-1 ... Added ARTIC v4.1 primer set information	2022-02-10 19:17:47 +00:00
James Fellows Yates	88ddc9eee7	fffff	2022-02-10 11:34:57 +01:00
James Fellows Yates	d7d0f5cecc	Change base time	2022-02-10 11:32:49 +01:00
James Fellows Yates	dbd78f8075	Re add .	2022-02-10 11:26:18 +01:00
James Fellows Yates	dd94895f16	remove quotes	2022-02-10 11:22:45 +01:00
James Fellows Yates	39c2d9b25b	Oops	2022-02-10 11:19:16 +01:00
James Fellows Yates	c0ee3225ad	Add times for 365d	2022-02-10 11:02:52 +01:00
Thiseas C. Lamnidis	fa4075c2a0	Removed all time limits	2022-02-10 10:00:18 +01:00
James A. Fellows Yates	64355b84d2	Merge pull request #325 from jfy133/eva-update ... Read add empty BAM exit code for qualimap 255 for eager @ EVA	2022-02-08 11:28:36 +01:00
James A. Fellows Yates	2b06293f64	Read add empty BAM exit code for qualitmap 255	2022-02-08 11:15:17 +01:00
James A. Fellows Yates	8d286e3b69	Merge pull request #324 from jfy133/eva-update ... New attempt of workaround SGE + Java incompatibility for eager @ EVA	2022-02-06 20:02:03 +01:00
James A. Fellows Yates	8c5a54ac9f	Update conf/pipeline/eager/eva.config	2022-02-06 19:37:53 +01:00
James A. Fellows Yates	aa525c6ebf	Allow exit code 1 retry for all java processes	2022-02-06 09:07:53 +01:00
Stevin Wilson	dbb71161c5	Added ARTIC v4.1 primer set information	2022-02-04 15:31:51 -05:00
phue	7bf6f284fa	cbe: lower the threshold for switching to m queue	2022-02-04 10:33:00 +01:00
phue	49810a69b3	cbe: add gpu support ... just in case.. note that this will need --nv in containerOptions in order to mount cuda libs into the container	2022-02-04 10:31:58 +01:00
phue	52b6f7da21	update anaconda module ... not sure why a binary distribution needs a buildenv at all, but well	2022-02-04 10:18:59 +01:00
James A. Fellows Yates	81fe720b00	Update eva.config	2022-02-04 09:31:33 +01:00
James A. Fellows Yates	86a9042eac	Update eva.config	2022-02-04 09:25:01 +01:00
Combiz Khozoie	81a273c730	Update imperial_mb.config ... Dropped support for pqmedbio-large which is not currently available.	2022-02-03 18:31:02 +00:00
Combiz Khozoie	2bdf5863d9	Update imperial.config ... Removed my contact details. Users can request help on the nf-core slack.	2022-02-03 18:28:11 +00:00
Combiz Khozoie	731f86e7f1	Update imperial_mb.config ... Removed my contact details. Users can request help on the nf-core slack.	2022-02-03 18:27:49 +00:00
Combiz Khozoie	453080f282	Update imperial.config ... Removed my contact details. Users can request help on the nf-core slack.	2022-02-03 18:26:30 +00:00
James A. Fellows Yates	50aafc6410	Update eva.config	2022-02-03 17:03:10 +01:00
James A. Fellows Yates	e02196d6ad	Update eva.config	2022-02-03 17:02:34 +01:00
James A. Fellows Yates	0e41349324	Update eva.config	2022-02-03 17:01:54 +01:00
Michael Borg	cc380ce9a1	Update mpcdf.config ... Added polling frequencies to the config as requested by MPCDF admin. Also updated the number of (real) cores on Raven.	2022-02-02 13:33:03 +01:00
James Fellows Yates	2562a2f563	Remove virtual free	2022-02-02 08:06:00 +01:00
James A. Fellows Yates	8739aabbf0	Bump markduplicates by default	2022-02-02 08:00:13 +01:00
Austyn Trull	1c9e1bf8a1	Fixing syntax in cheaha profile	2022-01-28 14:18:57 -06:00
Lara Ianov	9c0d550222	max_memory increase to reflect largemem	2022-01-28 11:45:13 -06:00
Austyn Trull	06541411dd	Initial commit of cheaha profile	2022-01-28 11:37:42 -06:00
Harshil Patel	9792226f5c	Update genomes.config	2022-01-27 12:45:41 +00:00
Praveen Raj S	5c1afd56bf	Added genome parameter ... Added genome parameter to the config file	2022-01-20 22:25:31 +01:00
Harshil Patel	cd6b8e0f17	Add --nextclade_dataset params	2022-01-17 16:51:55 +00:00
Harshil Patel	f26c465bd4	Add Nextclade genome details to viralrecon genome config	2022-01-17 11:27:10 +00:00
James A. Fellows Yates	5fd5c43906	Update eva.config	2022-01-14 07:03:05 +01:00
Maxime U. Garcia	61682f33b3	Merge pull request #310 from nf-core/praveenraj2018-patch-1 ... Updated sentieon version through a new module file	2022-01-10 12:04:20 +01:00
ameynert	0f56588acc	Added memory & cluster options specification for eddie sarek config	2022-01-06 10:15:34 +00:00
praveenraj2018	53ab5ee34f	Updated sentieon version through a new module file ... A local module file has been created to run the latest version of Sentieon. Doing this change, as the new version of Sentieon has only a dependency library update, hence it should not break the Sentieon pipeline. Tested locally with a test.conf having the new process block.	2021-12-21 15:21:59 +01:00
Kevin Brick	1abb1c2d95	Merge pull request #309 from kevbrick/master ... Added config for NIH Biowulf Cluster	2021-12-20 13:05:19 -05:00
Kevin Brick	82c7d553a7	Update bind-paths	2021-12-20 11:29:09 -05:00
Kevin Brick	87e4ece034	Add files via upload	2021-12-17 00:36:51 -05:00
Venkat Malladi	306c802b4e	Fix name of Params	2021-12-16 09:27:23 -06:00
PCQ	698555f801	Rename marvin.conf to marvin.config	2021-12-15 14:44:05 +01:00
praveenraj2018	0557f4e062	Renamed star_index directory	2021-12-14 21:15:12 +01:00
Maxime U. Garcia	5e92e2ef11	Update conf/pipeline/rnavar/munin.config	2021-12-14 16:10:31 +01:00
Praveen	cc1fe5b5a0	Addressed review feedback	2021-12-14 03:58:54 +01:00
Praveen	b4d5330c0e	Added rnavar pipeline config for Munin	2021-12-14 03:52:37 +01:00
PCQ	3a61adb69b	Rename Marvin.conf to marvin.conf	2021-12-13 11:38:48 +01:00
PCQ	50d90cd686	Marvin Cluster addition ... Added the config for the Marvin cluster of the Universitat Pompeu Fabra (UPF)	2021-12-10 17:11:43 +01:00
James A. Fellows Yates	55f452d81e	Update eva.config	2021-12-07 09:27:28 +01:00
James Fellows Yates	e8252ad61c	Reintroduce bionode8, bump overhead for flagstat	2021-12-03 08:36:31 +01:00
James Fellows Yates	06b40798c0	Exclude bionode8	2021-12-02 10:35:35 +01:00
Phil Ewels	4785ceccba	Merge pull request #245 from ikeller/unibe_ibu ... Unibe ibu	2021-11-19 00:56:25 +01:00
Phil Ewels	291fcb20a5	Merge pull request #297 from vsmalladi/azure ... Add in template for Azure Workflow	2021-11-19 00:55:54 +01:00
Venkat Malladi	72ccd44ad6	Remove storage name.	2021-11-18 17:52:51 -06:00
Venkat Malladi	ed4c1d5f22	Remove work_dir option.	2021-11-18 17:52:24 -06:00