553 commits

Author	SHA1	Message	Date
James Fellows Yates	b0e344846d	Changes after code review from @aidaanva	2021-08-04 10:37:49 +02:00
James Fellows Yates	76fc461670	Try new strategy for SGE/JAVA bs	2021-08-04 10:14:56 +02:00
Rogan Grant	f793ffaace	Updated iGenomes location	2021-08-03 15:10:54 -05:00
James A. Fellows Yates	00491de038	Update eva.config	2021-08-03 13:54:14 +02:00
Rogan Grant	24a2949fe2	Had executor options in wrong spot :(	2021-07-28 18:05:45 -05:00
Rogan Grant	6862fb8bfd	testing ternary operatory	2021-07-28 18:01:03 -05:00
Rogan Grant	bcc69fe83c	Enable use of himem nodes	2021-07-28 17:54:51 -05:00
Rogan Grant	ac11ca5568	Remove echo used for testing	2021-07-28 16:48:08 -05:00
Rogan Grant	3dd4f16d09	Added indicator for testing	2021-07-28 14:01:12 -05:00
Rogan Grant	09ed4d54b9	Just make command a single line for simplicity	2021-07-28 13:52:26 -05:00
Rogan Grant	09e0ea2674	typo	2021-07-28 13:46:40 -05:00
Rogan Grant	e1e0810d1b	Clean up module loading script	2021-07-28 13:44:48 -05:00
Rogan Grant	e2c566ed13	Testing "automounts"	2021-07-28 13:38:06 -05:00
Rogan Grant	f104250ff4	Removed comment	2021-07-28 13:34:49 -05:00
Rogan Grant	9df267a192	Merged duplicate params	2021-07-28 13:27:17 -05:00
Rogan Grant	ff6823ec1d	removed unnecessary space	2021-07-28 13:22:52 -05:00
Rogan Grant	9957e9eea1	Version 1 of custom config with queue-switching for long jobs and module loading	2021-07-28 13:11:02 -05:00
Barry digby	70b2644c9a	.	2021-07-27 17:39:37 +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	4f962260d0	s	2021-07-27 17:08:53 +01:00
Barry digby	04c0da5a2f	nuig confg (lugh)	2021-07-27 17:05:27 +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
Barry digby	24a4119e43	memory test	2021-04-29 14:24:57 +01:00
Barry digby	aeb0346cce	.	2021-04-28 20:14:32 +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
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
Asaf Peer	a0c8a9ec8f	updated jax resources	2021-04-12 16:00:34 -04:00
Phil Ewels	2f77d16b70	Merge pull request #220 from ewels/master ... UPPMAX: Avoid undefined parameter warnings	2021-04-08 15:06:00 +02:00
James A. Fellows Yates	161c3a33d4	Merge branch 'master' into eva	2021-04-07 19:28:16 +02:00
James A. Fellows Yates	ce465cca57	Apply suggestions from code review ... Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>	2021-04-07 19:27:24 +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
ameynert	0ab9edde72	Delete conf/pipeline/atacseq directory ... Pipeline-specific config not supported yet by ATAC-seq pipeline	2021-04-07 09:24:30 +01:00
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
James Fellows Yates	d69af0f287	Merging	2021-04-06 16:42:22 +02:00
phue	60ae267e43	use SLURM_CLUSTERS env var ... this seems to be more reliable for queue checking than using the clusterOptions directive. See https://github.com/nextflow-io/nextflow/issues/807	2021-04-06 11:35:01 +02:00
ameynert	6e201a71f4	ATAC-seq pipeline config ... Java processes with overhead memory requirements	2021-03-30 16:31:00 +01:00
ameynert	e5f2a63079	Java overhead processes list updated ... Added all processes calling GATK for Mutect2 variant calling	2021-03-30 16:21:53 +01:00
ameynert	adfb5366b9	Java overhead process list updated ... Added HaplotypeCaller and GenotypeGVCFs to set of processes that need Java overhead	2021-03-30 16:15:17 +01:00
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
Phil Ewels	d34bc40841	UPPMAX: add to schema_ignore_params	2021-03-26 15:22:57 +01:00
Phil Ewels	eccc9ea8d5	Define params.project and params.clusterOptions in uppmax config	2021-03-26 15:20:32 +01:00
Santiago Lacalle	e2c583d558	Remove "/rdsgpfs" ... "/rdsgpfs" symlink will not be present on all nodes. Without that mount the container creation will fail.	2021-03-25 12:38:15 +00:00
Alexander Peltzer	26b5904df1	Merge pull request #218 from asafpr/master ... added jax singularity cache dir	2021-03-24 17:39:03 +01:00
Asaf Peer	922ab87eb0	added jax singularity cache dir	2021-03-24 11:25:47 -04:00
Phil Ewels	bfab371c94	Merge branch 'master' into master	2021-03-24 12:36:15 +01:00
ameyner2	da8cf2f207	Added pipeline-specific config files for rnaseq and sarek	2021-03-24 10:46:26 +00:00
Asaf Peer	9b2d5bfead	Merge pull request #216 from asafpr/master ... Added JAX conf	2021-03-24 03:31:14 -04:00
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
Edmund Miller	a6975cdd4e	fix(ganymede): large => high ... Co-authored-by: drpatelh <drpatelh@users.noreply.github.com>	2021-03-22 12:42:56 -05:00
Edmund Miller	34ccce9531	fix(ganymede): Add process resources ... Trimgalore though it can be a bottom neck, doesn't require the 1 big memory node we have and can be run on the genomics queue.	2021-03-21 21:47:59 -05:00
Edmund Miller	4570718b12	fix(ganymede): Add TMPDIR and SINGULARITY_CACHEDIR env variables	2021-03-21 21:45:39 -05:00