153 commits

Author	SHA1	Message	Date
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