847 commits

Author	SHA1	Message	Date
James Fellows Yates	df0429ce9d	Replace oracle specific _JAVA_OPTIONS to portable JAVA_TOOLS_OPTIONS	2022-06-03 14:20:39 +02:00
Phil Ewels	b51059a3ae	Merge branch 'master' into config_ucph-mjolnir_ash	2022-06-03 13:21:36 +02:00
James A. Fellows Yates	7353fb257d	Merge pull request #380 from jfy133/taxprofiler ... Add MAG @ EVA profile	2022-06-03 12:54:47 +02:00
James Fellows Yates	5a67eba04c	Add MAG @ EVA profile	2022-06-03 12:41:08 +02:00
Åshild J. Vågene	9b9a6f0188	Update and rename holo_globe to mjolnir_globe	2022-06-02 15:09:52 +02:00
Åshild J. Vågene	6d9cc91c5f	Update holo_globe	2022-06-02 15:03:47 +02:00
Åshild J. Vågene	64fe4677b1	Update holo_globe	2022-05-31 15:26:23 +02:00
Åshild J. Vågene	0b51552e88	Update holo_globe	2022-05-31 15:23:43 +02:00
Emil Bertilsson	80e2a50a2f	Merge pull request #378 from raysloks/feat/hasta_java_memory_fix ... Feat/hasta java memory fix	2022-05-30 14:40:52 +02:00
Emil	8453f6b41a	Moves qualimap arg to pipeline-specific config	2022-05-30 12:58:12 +02:00
Emil	29fa08c434	Adds _JAVA_OPTIONS to singularity whitelist	2022-05-30 11:07:24 +02:00
Emil	19497a4183	Makes qualimap fix work for most memory amounts	2022-05-30 11:06:48 +02:00
Åshild J. Vågene	bb25c77e7c	Update holo_globe	2022-05-20 17:01:30 +02:00
Åshild J. Vågene	d3e5c79fb4	Create holo_globe	2022-05-20 15:44:20 +02:00
Nicolas Vannieuwkerke	c2b26a734d	automated the internal cache dir location for singularity	2022-05-20 09:48:19 +02:00
Nicolas Vannieuwkerke	cc86e6b270	Added the VSC UGent profile	2022-05-20 09:12:18 +02:00
Sarah Guinchard	be9711731a	Merge pull request #375 from nf-core/ifb_core-config-update ... Ifb core config update	2022-05-13 14:45:44 +02:00
Sarah Guinchard	3538f8511a	removed comment	2022-05-12 11:02:42 +02:00
sofstam	54b3cda34d	Add review suggestion	2022-05-12 11:00:26 +02:00
Sarah Guinchard	6bb7c1a422	Update config file with queue & correct ressources	2022-05-12 10:55:00 +02:00
sofstam	c59149d64c	Update docs for hasta config	2022-05-12 10:47:03 +02:00
James Fellows Yates	e1f780d976	Add taxprofiler for eVA	2022-05-12 07:54:17 +01:00
sofstam	5bc6ed90bd	Add hasta config for taxprofiler	2022-05-11 11:13:31 +02:00
Thiseas C. Lamnidis	d09f5fc116	Update eva.config ... eigenstrat_snp_coverage also loads pandas	2022-05-06 15:12:04 +02:00
James A. Fellows Yates	8fbfcfe256	Merge pull request #371 from jfy133/master ... Rename custom log file for EVA	2022-05-06 14:02:03 +02:00
James A. Fellows Yates	95d18270e8	Update eva.config	2022-05-06 13:57:11 +02:00
Emil	e938f3606f	Removes the new SGE clusterOptions for now	2022-05-05 14:09:45 +02:00
Harshil Patel	20c826fd50	Update retry strategy for preemptible instances on GCP	2022-05-05 11:10:05 +01:00
Emil	8b9744723c	Fixes hasta java memory issues	2022-05-04 14:13:24 +02:00
Thiseas C. Lamnidis	209601f782	missing bracket	2022-05-04 13:08:13 +02:00
Thiseas C. Lamnidis	a42c4344ad	Exclude bionode 06 for software versions	2022-05-03 18:30:42 +02:00
Thiseas C. Lamnidis	79e227aa4e	Update eva.config	2022-05-03 16:42:21 +02:00
Thiseas C. Lamnidis	085726d081	Update eva.config	2022-05-03 16:36:05 +02:00
Thiseas C. Lamnidis	4592969613	memory for get_software_versions in MB.	2022-05-03 16:30:04 +02:00
Thiseas C. Lamnidis	79ad571319	Update eva.config	2022-05-03 16:25:48 +02:00
Thiseas C. Lamnidis	04226692fe	Update eva.config	2022-05-03 16:21:35 +02:00
Thiseas C. Lamnidis	57095fe79f	Update eva.config ... Set max heap size for java jobs in `get_software_versions`. Limited OpenBLAS threading for python jobs that use numpy/pandas.	2022-05-03 16:12:20 +02:00
James A. Fellows Yates	b5d9b79377	Merge branch 'nf-core:master' into master	2022-05-02 13:59:18 +02:00
James A. Fellows Yates	bf658abc77	Update eva.config	2022-05-02 13:59:13 +02:00
Ramprasad Neethiraj	40c965c76b	fix sentieon errors	2022-04-29 00:20:57 +02:00
Alex Rajewski	69d1a14894	basic Cedars-Sinai HPC config file	2022-04-22 10:17:13 -07:00
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	3e3e2be04b	remove duplicate entries	2022-04-22 00:09:29 +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
James A. Fellows Yates	576351219a	Update eva.config	2022-03-29 12:47:46 +02:00
James A. Fellows Yates	9e502025b9	Merge pull request #358 from aidaanva/master ... Update eva.config bigmem.q	2022-03-28 09:11:18 +02:00
Mahesh Binzer-Panchal	3a7f7f431e	Execute sinfo with bash shell	2022-03-25 13:58:37 +00:00
Aida Andrades Valtueña	b9da0b4f00	Update eva.config ... Update eva.config to send big memory jobs (>700G) to the bigmem queue	2022-03-25 09:36:29 +01:00
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	962d86d604	Merge pull request #346 from sagc-bioinformatics/sahmri ... Added SAHMRI profile	2022-03-18 13:01:36 +01:00
Nathan S. Watson-Haigh	30f710ada4	Add debug profile	2022-03-17 13:38:43 +10:30
Praveen Raj S	1d4f254e43	Update munin.config	2022-03-16 14:37:28 +01:00
Praveen Raj S	9747d5fe15	Added PileupSummariesForMutect2 in CPU limit list ... Add PileupSummariesForMutect2 to the list to run with less threads. Changed the MaxForks to 12 Tested on an internal sample and it worked!	2022-03-16 14:36:25 +01:00
Alexander Peltzer	d510cb254e	Merge pull request #165 from ewels/fix-show-profiles ... Set params.custom_config_base in nextflow.config	2022-03-15 17:13:24 +01:00
Praveen Raj S	a844335942	Update conf/munin.config ... Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>	2022-03-15 16:59:06 +01:00
Praveen Raj S	cb96c4bd2d	Update conf/munin.config ... Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>	2022-03-15 16:56:11 +01:00
Praveen Raj S	13c66f7e98	Update conf/munin.config ... Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>	2022-03-15 16:56:03 +01:00
Praveen Raj S	50c4610345	Adjusted time and maxforks for Mutect2	2022-03-15 16:29:19 +01:00
Alexander Peltzer	3e4fae71a4	Merge branch 'master' into fix-show-profiles	2022-03-15 14:52:29 +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
Nathan S. Watson-Haigh	a0f5ac7445	Added references subdir to igenomes_base	2022-03-15 11:41:51 +10:30
James A. Fellows Yates	4670f8bf0c	Update eva.config	2022-03-14 14:56:01 +01:00
James A. Fellows Yates	a2e2e94333	Merge pull request #344 from njspix/vai ... Add VAI configuration	2022-03-14 14:36:00 +01:00
Nathan Watson-Haigh	cc55026751	Add singularity to PATH	2022-03-13 07:39:31 +10:30
Nathan Watson-Haigh	2f0b022571	Fixed typos	2022-03-13 00:08:42 +10:30
Nathan Watson-Haigh	b638694bd0	Added SAHMRI HPC profile	2022-03-12 21:17:33 +10:30
Matiss	6c79c75eec	Merge pull request #290 from maxozo/master ... added leicester profile	2022-03-11 09:21:09 +00:00
Nathan Spix	d067f61329	remove extra spaces	2022-03-07 15:22:18 -05:00
Spix	17c77ad516	update singularity command	2022-03-07 15:13:26 -05:00
Spix	c97c48ae5b	update singularity command	2022-03-07 15:11:45 -05:00
Spix	429c7b4fa8	initial commit	2022-03-07 15:01:46 -05:00
Alexander Peltzer	d0d86bfb2a	Merge pull request #339 from jfy133/rnaseq_mpcdf ... Add RNASEQ specific config for MPCDF	2022-03-07 13:59:08 +01:00
James A. Fellows Yates	975fca6721	Apply suggestions from code review	2022-03-07 13:51:00 +01:00
Natalia Zajac	97058995ef	Update on singularity cache	2022-03-07 12:37:01 +01:00
Natalia Zajac	e07a0e548e	Config Addition	2022-03-04 12:16:01 +01:00
James Fellows Yates	70318c3b2a	Tweak eager settigs	2022-03-03 14:29:30 +01:00
James A. Fellows Yates	546393ed18	Apply suggestions from code review	2022-03-03 14:22:35 +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 Fellows Yates	7112e74b73	Tweak settings based on latest batch specs	2022-03-03 13:43:40 +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	a6c12d8edc	Merge pull request #322 from U-BDS/master ... Add UAB Cheaha profile	2022-03-01 08:29:54 +01:00
PCQ	1ff92db608	Merge branch 'nf-core:master' into master	2022-02-28 14:50:41 +01:00