480 commits

Author	SHA1	Message	Date
ameynert	238d6e5e96	Added cacheDir to singularity in eddie profile	2021-07-23 09:33:02 +01:00
ameynert	2112168420	Set BLASTDB_LMDB_MAP_SIZE ... This environment variable needs to be set in order to prevent memory allocation errors in the MAKEBLASTDB process.	2021-07-22 15:07:19 +01:00
ameynert	4ceb369af5	eddie.config for viralrecon pipeline	2021-07-21 12:10:43 +01:00
Maxime U. Garcia	30e058abf0	Merge branch 'master' into master_kraken	2021-07-20 09:26:56 +02:00
Harshil Patel	962dca7a46	Add ARTIC v1200 primers to genomes config for viralrecon	2021-07-12 12:24:49 +01:00
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
Harshil Patel	69f63a006d	Merge pull request #254 from drpatelh/articv4 ... Add ARTIC v4 primers to genomes config for viralrecon	2021-07-01 12:31:02 +01:00
Gisela Gabernet	aae0f0bf07	Merge pull request #255 from ggabernet/master ... update cfc configs	2021-07-01 10:59:25 +02:00
ggabernet	d59d099fe8	remove load module in cfc configs	2021-07-01 10:52:54 +02:00
James A. Fellows Yates	5f4b915ae8	Update eva.config	2021-06-29 11:31:00 +02:00
Harshil Patel	93cfc48afd	Add ARTIC v4 primers to genomes config	2021-06-21 21:04:16 +01:00
Edmund Miller	21e1037e0c	docs(sysbio): Add rnaseq specific docs	2021-06-17 09:18:45 -05:00
Edmund Miller	e35c5fd1d8	fix(sysbio): Add nf-core params	2021-06-17 08:32:31 -05:00
Edmund Miller	41ae99d34a	feat(sysbio): Add cleanup	2021-06-17 08:17:55 -05:00
Edmund Miller	14a2106c63	fix(sysbio): Move rnaseq specific things to pipeline config	2021-06-17 08:14:48 -05:00
Edmund Miller	472082254a	fix(sysbio): Add Star resources	2021-06-16 21:18:48 -05:00
Edmund Miller	b11f137901	fix(sysbio): Leave igenomes unfinished	2021-06-16 21:18:28 -05:00
Edmund Miller	04d0b27e81	fix(sysbio): Reduce memory on high processes	2021-06-16 21:17:40 -05:00
Edmund Miller	2b58a62a9b	feat(utd): Add initial sysbio config	2021-06-11 14:50:58 -05:00
ggabernet	c3385593cb	revert cfc config	2021-06-11 14:59:09 +02:00
mseybold	f196de8246	Update cfc.config ... singularity is now installed natively on the nodes, so no more need for a module here	2021-06-10 12:34:58 +02:00
James A. Fellows Yates	756f067213	Merge pull request #248 from jfy133/eva ... Fix MakeSeqDict eager @ eva	2021-06-07 13:26:05 +02:00
James A. Fellows Yates	da8e002969	Merge pull request #247 from jfy133/shh-fx ... Fix eageR@SHH HOPS profile human ref path	2021-06-07 10:55:01 +02:00
James A. Fellows Yates	fc8b1162c1	Fix HOPS huamn ref path	2021-06-07 10:48:35 +02:00
James A. Fellows Yates	5bf57894a5	Merge pull request #246 from jfy133/shh-update ... Make eager@SHH big_data go by default to medium via run time	2021-06-04 12:32:28 +02:00
James A. Fellows Yates	31d46cb0a9	Make big_data go by default to medium via run time	2021-06-04 12:22:54 +02:00
Øyvind Almelid	c75ceec35d	Merge pull request #244 from oalmelid/master ... eddie.conf: Add TMPDIR and mount for it to singularity configuration + Migrate to BioinformaticsResources for genomes.	2021-05-25 10:03:05 +01:00
Øyvind Almelid	f6578f727d	Add TMPDIR and mount for it to singularity configuration	2021-05-25 09:54:08 +01:00
Olga Botvinnik	2ac4693421	Merge pull request #243 from nf-core/olgabot-patch-1 ... executor.cli --> aws.batch.cliPath	2021-05-20 10:34:55 -07:00
MaxUlysse	05548bdb75	fix: forgotten }	2021-05-20 09:37:48 +02:00
Olga Botvinnik	8166e0f606	executor.cli --> aws.batch.cliPath	2021-05-19 13:36:15 -07:00
MaxUlysse	73fcc4495a	feat: update owner of profile	2021-05-19 20:46:52 +02:00
Phil Ewels	9c4830c8d5	Merge pull request #238 from nf-core/hebbe-config-fix	2021-05-19 17:46:52 +02:00
James A. Fellows Yates	3bcd55966d	Update eva.config	2021-05-05 11:39:33 +02:00
James A. Fellows Yates	f2413553a3	Merge pull request #240 from jfy133/shh ... eager@SHH Add additional retry allowance for silly big data in markdups	2021-05-05 10:52:58 +02:00
James A. Fellows Yates	a849fe991c	Add additional retry allowance for silly big data in markdups	2021-05-04 21:43:19 +02:00
Maxime U. Garcia	77bd7f567f	Merge pull request #228 from asafpr/master ... updated jax resources	2021-05-02 14:47:19 +02:00
Phil Ewels	76b62b478d	Fix hebbe withName regex	2021-04-29 23:06:56 +02:00
Alexander Peltzer	c12c373969	Merge pull request #235 from aunderwo/cambridge ... Add Cambridge University HPC config	2021-04-25 10:40:56 +02:00
Gisela Gabernet	4e9e5d2c67	Merge branch 'master' into cfc_sarek	2021-04-23 16:47:04 +02:00
Anthony Underwood	8b3951b244	Create cambridge.config	2021-04-22 16:00:37 +01:00
Anthony Underwood	351c5773f0	Add queue limits for 'normal'	2021-04-22 11:59:34 +01:00
Anthony Underwood	7d8770af1a	Create sanger.config	2021-04-21 16:39:55 +01:00
phue	b225a0555a	biohpc_gen: update software tree path	2021-04-21 10:08:00 +02:00
James A. Fellows Yates	eacdf89e53	Update eva.config	2021-04-20 13:17:35 +02:00
James A. Fellows Yates	b9a00f7926	Update mpcdf.config	2021-04-15 22:27:07 +02:00
Harshil Patel	7ac66dcd72	Update crick.config	2021-04-13 17:07:02 +01:00
Combiz Khozoie	c571c05ab9	Merge pull request #219 from slacalle/patch-2 ... Imperial College | Remove "/rdsgpfs"	2021-04-13 15:28:00 +01:00
MaxUlysse	3918e0aa9d	feat: remove kraken profile	2021-04-13 15:14:14 +02:00