193 commits

Author	SHA1	Message	Date
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
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
James A. Fellows Yates	50aafc6410	Update eva.config	2022-02-03 17:03:10 +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
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