138 commits

Author	SHA1	Message	Date
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