229 commits

Author	SHA1	Message	Date
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
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	14a2106c63	fix(sysbio): Move rnaseq specific things to pipeline config	2021-06-17 08:14:48 -05:00
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
MaxUlysse	73fcc4495a	feat: update owner of profile	2021-05-19 20:46:52 +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
Gisela Gabernet	4e9e5d2c67	Merge branch 'master' into cfc_sarek	2021-04-23 16:47:04 +02:00
James A. Fellows Yates	eacdf89e53	Update eva.config	2021-04-20 13:17:35 +02:00
James A. Fellows Yates	161c3a33d4	Merge branch 'master' into eva	2021-04-07 19:28:16 +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
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
ameyner2	da8cf2f207	Added pipeline-specific config files for rnaseq and sarek	2021-03-24 10:46:26 +00:00
Rike	6221b67bcf	Give Strelka a complete compute node	2021-03-18 11:11:02 +01:00
Rike	b1846af9d3	reduce mapping resource further to compute node	2021-03-18 11:10:00 +01:00
FriederikeHanssen	67c93a4743	Update conf/pipeline/sarek/cfc.config ... Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>	2021-03-18 11:06:38 +01:00
Rike	b70097e495	remove new line	2021-03-17 15:46:18 +01:00
Rike	bb124a9be8	Reduce vc to run on compute	2021-03-11 16:11:41 +01:00
FriederikeHanssen	79ddbe1fea	Add missing bracket	2021-03-11 09:29:03 +01:00
FriederikeHanssen	0057132e02	remove check_reource statement	2021-03-11 09:27:08 +01:00
FriederikeHanssen	eb9012919c	Set values for processes with max_mem/max_cpus	2021-03-10 11:16:18 +01:00
drpatelh	01a4f8559e	Update links to be consistent	2021-02-16 13:17:16 +00:00
Harshil Patel	6ffaf922c5	Update genomes.config	2021-02-16 10:28:32 +00:00
Harshil Patel	4de0855218	Update genomes.config	2021-02-15 18:48:03 +00:00
drpatelh	9d500cf679	Reorder params	2021-02-15 17:02:26 +00:00
drpatelh	f283dfb2dc	Add ARTIC primer sets to genome config	2021-02-15 16:58:30 +00:00
James Fellows Yates	537f52a640	Add MPI-EVA profile	2021-02-14 17:50:20 +01:00
James A. Fellows Yates	86566ddd3b	Merge pull request #204 from jfy133/master ... Add a 'big_data' profile for eager @ SHH	2021-02-04 15:07:52 +01:00
James A. Fellows Yates	e32f1e46ff	Update shh.config	2021-02-04 08:13:16 +01:00
James A. Fellows Yates	c515a401c7	Update shh.config	2021-02-04 08:06:35 +01:00
James A. Fellows Yates	82fe8a04be	Update shh.config	2021-02-04 08:02:33 +01:00
James A. Fellows Yates	e7ac0bae13	Update shh.config	2021-02-04 08:00:57 +01:00
James A. Fellows Yates	eb725f9ea3	Update shh.config	2021-02-03 20:13:09 +01:00
James A. Fellows Yates	1c25cb033b	Add big_data profile	2021-01-19 13:53:01 +01:00
James A. Fellows Yates	a4c55b3ea9	Fix time limit 0-9 typo	2021-01-06 10:44:12 +01:00
Combiz Khozoie	a61992d144	Added institutional configs for Imperial and Imperial MEDBIO. Added institutional pipeline configs for scflow for Imperial and Imperial MEDBIO	2020-12-18 10:21:26 +00:00
Emelie Nilsso	febf38dd8e	Removed an old process so that only relevant processes are included	2020-11-26 13:38:47 +01:00
Emelie Nilsso	d61ed01d2d	Updated process names according to ampliseq main.nf	2020-11-25 17:50:30 +01:00
Emelie Nilsso	37e7cfae2c	Removed unnecessary code that was used to troubleshoot	2020-11-24 07:14:23 +01:00
Emelie Nilsso	2ea06ffab8	Modified uppmax and ampliseq specific config to fit with the divided preparation of the database	2020-11-23 21:20:36 +01:00
James A. Fellows Yates	804f53c58c	Merge pull request #178 from jfy133/master ... Add Max Planck Computing and Data Facility Cobra/Raven Clusters	2020-10-22 13:34:11 +02:00
MaxUlysse	8c0cc4b9ec	code polishing	2020-09-25 09:57:50 +02:00
MaxUlysse	81f910cc95	add specific BamQC config	2020-09-25 09:49:43 +02:00
MaxUlysse	fbe7bd133a	update uppmax specific sarek config	2020-09-25 08:33:53 +02:00
James A. Fellows Yates	11f1fb71db	Update mpcdf.config	2020-09-16 10:21:58 +02:00
James A. Fellows Yates	c6f7573d01	Update mpcdf.config	2020-09-15 17:48:54 +02:00
James A. Fellows Yates	bf87ec24e7	Update mpcdf.config	2020-09-15 17:45:38 +02:00
James A. Fellows Yates	3b7902d11b	Mad multi-core increase CPUs on retry	2020-09-06 08:23:35 +02:00
James A. Fellows Yates	4335e5deb7	Update mpcdf.config	2020-09-04 20:17:09 +02:00