289 commits

Author	SHA1	Message	Date
Ramprasad Neethiraj	40c965c76b	fix sentieon errors	2022-04-29 00:20:57 +02:00
James A. Fellows Yates	c1425c6c01	Merge pull request #364 from jfy133/eva-update ... Update eager @ eva.config to allow retry on post-processing FASTQ	2022-04-22 11:47:10 +02:00
Ramprasad Neethiraj	9da85209f2	change bcftools output format	2022-04-22 11:05:56 +02:00
Ramprasad Neethiraj	447b3ee05d	add beforescript for sentieon	2022-04-22 11:03:09 +02:00
James A. Fellows Yates	a086878c0b	Update eva.config	2022-04-22 10:47:04 +02:00
Ramprasad Neethiraj	d39bec05dc	fix typo	2022-04-19 13:21:51 +02:00
Ramprasad Neethiraj	32207a2402	update path so that the sentieon version is explicit	2022-04-19 11:42:05 +02:00
Ramprasad Neethiraj	6fad232232	sentieon env variable	2022-04-19 11:27:35 +02:00
Ramprasad Neethiraj	afe935c2d0	include stub profile	2022-04-15 15:27:41 +02:00
Praveen Raj S	edaad1cd18	Update: sentieon version ... Sentieon version has been updated to 202112.02.	2022-04-07 12:36:01 +02:00
James A. Fellows Yates	44238471cf	Update eva.config	2022-03-31 13:12:50 +02:00
James Fellows Yates	2277b541a3	Re-add bash bin specification	2022-03-31 11:06:53 +02:00
James A. Fellows Yates	8ad4ddac6a	Merge branch 'master' into fix-eva	2022-03-29 12:50:54 +02:00
James Fellows Yates	3d2a612b39	Remove setting of bash in clusterOotions	2022-03-29 12:48:37 +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
James A. Fellows Yates	1b5037ce5e	Update eva.config	2022-03-15 07:49:06 +01:00
James A. Fellows Yates	1565b2ce63	Update eva.config	2022-03-15 07:42:23 +01:00
James A. Fellows Yates	f725b6c431	Apply suggestions from code review	2022-03-15 07:36:34 +01:00
James A. Fellows Yates	4670f8bf0c	Update eva.config	2022-03-14 14:56:01 +01:00
James A. Fellows Yates	975fca6721	Apply suggestions from code review	2022-03-07 13:51:00 +01:00
James Fellows Yates	70318c3b2a	Tweak eager settigs	2022-03-03 14:29:30 +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 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	46f046d477	Update eva.config	2022-02-28 14:00:37 +01:00
Mei Wu	dcba537d15	picard md is single threaded	2022-02-21 16:19:17 +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
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	2b06293f64	Read add empty BAM exit code for qualitmap 255	2022-02-08 11:15:17 +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
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	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
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
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
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
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
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
James A. Fellows Yates	ffdb0a937f	Take previous working one I think	2021-10-18 10:58:06 +02:00
James A. Fellows Yates	b269a577e6	Revert 1240k	2021-10-18 10:52:28 +02:00
Thiseas C. Lamnidis	e741ecb7a7	Update eva.config	2021-10-13 13:04:41 +02:00
Thiseas C. Lamnidis	92648c1c1f	added 1240k profile	2021-10-12 15:12:49 +02:00
James A. Fellows Yates	73b6b74c69	Merge pull request #279 from pierrespc/master ... Added Configuration files for running in Maestro HPC at Pasteur Institute, Paris	2021-10-08 19:15:47 +02:00
pierrespc	035ab61f61	added unlimitedtime profile to maestro; changed cache for bwa process	2021-10-08 09:05:46 +02:00
pierrespc	1621585558	improving documentation	2021-10-04 16:08:33 +02:00
pierrespc	e5d4a357c5	clean doc	2021-10-04 15:08:01 +02:00
Rike	f6e16f2872	Add check_resource to respect max_resource/max_cpus	2021-10-04 10:14:02 +02:00
pierrespc	f6266879d6	edited maestronuclear and maestromitocondrial configs. The latter has not been optimized yet	2021-09-29 13:47:35 +02:00
pierrespc	b71df6fe57	renamed eager pipeline config file	2021-09-29 13:22:07 +02:00
pierrespc	9ea3e2096a	long and normal qos profiles defined now in an unique maestro config file. maestro.config also defined in pipeline/eager for ressources assignation to specific processes	2021-09-29 13:11:14 +02:00
Mei Wu	79a79f7d8d	added pipeline-specific config	2021-09-28 10:38:25 +02:00
James A. Fellows Yates	a7b1183065	Remove 1CPU for host removal fastq	2021-09-14 11:52:21 +02:00
James A. Fellows Yates	7c639ac934	Bump lib merge further	2021-09-09 14:47:20 +02:00
James A. Fellows Yates	0603aba342	Remove debugging stuff	2021-09-09 13:54:01 +02:00
James A. Fellows Yates	7ec12b6736	Update eva.config	2021-09-09 13:10:05 +02:00
James A. Fellows Yates	4286a3a342	Bump additional library merge memor	2021-09-08 15:16:40 +02:00
James A. Fellows Yates	59a0901b68	Add library merge steps to have overhead	2021-09-05 12:07:53 +02:00
James A. Fellows Yates	94cbb031c6	Update eva.config	2021-08-30 13:29:44 +02:00
James A. Fellows Yates	5fbd938bc1	Export user env too	2021-08-27 10:08:20 +02:00
James A. Fellows Yates	bcb844f896	Merge pull request #268 from jfy133/master ... Delete SHH profiles due to decommissioning	2021-08-23 14:08:13 +02:00
James Fellows Yates	59af7f0eee	Delete SHH profiles due to decommissioning	2021-08-20 10:15:39 +02:00
James A. Fellows Yates	6701354060	Add genotyping_ug to SGE fixes	2021-08-20 10:11:11 +02:00
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
James A. Fellows Yates	00491de038	Update eva.config	2021-08-03 13:54:14 +02:00
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
Harshil Patel	962dca7a46	Add ARTIC v1200 primers to genomes config for viralrecon	2021-07-12 12:24:49 +01:00
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
James A. Fellows Yates	5f4b915ae8	Update eva.config	2021-06-29 11:31:00 +02:00