841 commits

Author	SHA1	Message	Date
theoportlock	b240142cc3	Adds rosalind configuration	2021-09-08 14:33:39 +02:00
Rogan Grant	a7aca37bc8	Set autoMounts to true	2021-09-06 15:15:46 -05:00
Rogan Grant	b56b7b310b	Merge pull request #266 from RoganGrant/master ... Northwestern University Genomics Nodes (new add)	2021-09-06 13:26:49 -05:00
James A. Fellows Yates	39f54db097	Update container cache	2021-09-05 12:09:02 +02:00
James A. Fellows Yates	59a0901b68	Add library merge steps to have overhead	2021-09-05 12:07:53 +02:00
Rogan Grant	54298ca0f7	Merge branch 'nf-core:master' into master	2021-09-04 15:37:03 -05:00
rogangrant	a8d06ee356	Revert "Forgot a slash :(" ... This reverts commit d5601fea84.	2021-09-04 15:36:05 -05:00
Rogan Grant	d5601fea84	Forgot a slash :(	2021-09-04 15:19:32 -05:00
Rogan Grant	2c5e454d16	Updated iGenomes path for odd local structure on Quest	2021-09-04 15:13:41 -05:00
Marc Trunjer Kusk Nielsen	1bf2d436d4	Update computerome.config	2021-09-01 22:21:31 +02:00
Marc Trunjer Kusk Nielsen	e2d54cb56c	Update computerome.config	2021-09-01 22:06:56 +02:00
Marc Trunjer Kusk Nielsen	a1413ce18e	Update computerome.config	2021-09-01 21:47:48 +02:00
Marc Trunjer Kusk Nielsen	d4c71f0d8d	Update computerome.config	2021-09-01 13:22:31 +02:00
Marc Trunjer Kusk Nielsen	fdac67afbf	Create computerome.config	2021-08-31 13:58:39 +02:00
James A. Fellows Yates	94cbb031c6	Update eva.config	2021-08-30 13:29:44 +02:00
Patrick Hüther	6c4998fa8a	reduce max_memory to 1.8TB	2021-08-27 14:01:34 +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
Rogan Grant	f793ffaace	Updated iGenomes location	2021-08-03 15:10:54 -05:00
James A. Fellows Yates	00491de038	Update eva.config	2021-08-03 13:54:14 +02:00
Rogan Grant	24a2949fe2	Had executor options in wrong spot :(	2021-07-28 18:05:45 -05:00
Rogan Grant	6862fb8bfd	testing ternary operatory	2021-07-28 18:01:03 -05:00
Rogan Grant	bcc69fe83c	Enable use of himem nodes	2021-07-28 17:54:51 -05:00
Rogan Grant	ac11ca5568	Remove echo used for testing	2021-07-28 16:48:08 -05:00
Rogan Grant	3dd4f16d09	Added indicator for testing	2021-07-28 14:01:12 -05:00
Rogan Grant	09ed4d54b9	Just make command a single line for simplicity	2021-07-28 13:52:26 -05:00
Rogan Grant	09e0ea2674	typo	2021-07-28 13:46:40 -05:00
Rogan Grant	e1e0810d1b	Clean up module loading script	2021-07-28 13:44:48 -05:00
Rogan Grant	e2c566ed13	Testing "automounts"	2021-07-28 13:38:06 -05:00
Rogan Grant	f104250ff4	Removed comment	2021-07-28 13:34:49 -05:00
Rogan Grant	9df267a192	Merged duplicate params	2021-07-28 13:27:17 -05:00
Rogan Grant	ff6823ec1d	removed unnecessary space	2021-07-28 13:22:52 -05:00
Rogan Grant	9957e9eea1	Version 1 of custom config with queue-switching for long jobs and module loading	2021-07-28 13:11:02 -05:00
Barry digby	70b2644c9a	.	2021-07-27 17:39:37 +01:00
Barry digby	2b6e80561a	Merge branch 'master' of https://github.com/nf-core/configs into	2021-07-27 17:13:17 +01:00
Barry digby	4f962260d0	s	2021-07-27 17:08:53 +01:00
Barry digby	04c0da5a2f	nuig confg (lugh)	2021-07-27 17:05:27 +01:00
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
Maxime U. Garcia	30e058abf0	Merge branch 'master' into master_kraken	2021-07-20 09:26:56 +02:00
Harshil Patel	962dca7a46	Add ARTIC v1200 primers to genomes config for viralrecon	2021-07-12 12:24:49 +01:00
Gisela Gabernet	e2088a008d	Merge branch 'master' into master	2021-07-03 12:24:42 +02:00
ggabernet	ee2e8392ab	add aws_tower profile	2021-07-03 12:17:21 +02:00
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
Gisela Gabernet	aae0f0bf07	Merge pull request #255 from ggabernet/master ... update cfc configs	2021-07-01 10:59:25 +02:00
ggabernet	d59d099fe8	remove load module in cfc configs	2021-07-01 10:52:54 +02:00
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	41ae99d34a	feat(sysbio): Add cleanup	2021-06-17 08:17:55 -05:00
Edmund Miller	14a2106c63	fix(sysbio): Move rnaseq specific things to pipeline config	2021-06-17 08:14:48 -05:00
phue	45213cf6db	add note about upcoming upstream fix ... also refactor the closure to make it slightly more readable	2021-06-17 11:12:36 +02:00
Edmund Miller	472082254a	fix(sysbio): Add Star resources	2021-06-16 21:18:48 -05:00
Edmund Miller	b11f137901	fix(sysbio): Leave igenomes unfinished	2021-06-16 21:18:28 -05:00
Edmund Miller	04d0b27e81	fix(sysbio): Reduce memory on high processes	2021-06-16 21:17:40 -05:00
phue	f5c36dde3e	cbe: send SIGUSR2 upon job termination ... Previously, if a process hit the walltime limit and received SIGKILL from the slurm scheduler, singularity did not properly propagate such (soft) kill signal. This prevented the exit code to be caught, e.g for resubmission purposes. This commit introduces a workaround using slurms --signal directive to send SIGUSR2 to the singularity process itself (instead of container child processes, which presumably was happening before). Effectively, once a job reaches walltime limit, this will result in exitcode 140 which is typically caught by the errorStrategy in nf-core pipelines See also: https://slurm.schedmd.com/sbatch.html#OPT_signal https://github.com/nextflow-io/nextflow/issues/2163 https://github.com/nextflow-io/nextflow/issues/1561	2021-06-16 16:36:39 +02:00
Edmund Miller	2b58a62a9b	feat(utd): Add initial sysbio config	2021-06-11 14:50:58 -05:00
ggabernet	c3385593cb	revert cfc config	2021-06-11 14:59:09 +02:00
mseybold	f196de8246	Update cfc.config ... singularity is now installed natively on the nodes, so no more need for a module here	2021-06-10 12:34:58 +02:00
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
Øyvind Almelid	c75ceec35d	Merge pull request #244 from oalmelid/master ... eddie.conf: Add TMPDIR and mount for it to singularity configuration + Migrate to BioinformaticsResources for genomes.	2021-05-25 10:03:05 +01:00
Øyvind Almelid	f6578f727d	Add TMPDIR and mount for it to singularity configuration	2021-05-25 09:54:08 +01:00
Olga Botvinnik	2ac4693421	Merge pull request #243 from nf-core/olgabot-patch-1 ... executor.cli --> aws.batch.cliPath	2021-05-20 10:34:55 -07:00
ikeller	ae114dd142	edit max_time	2021-05-20 13:52:13 +02:00
ikeller	5a0ecbd81d	edit max_time	2021-05-20 13:48:59 +02:00
ikeller	6def686ab5	edit config	2021-05-20 13:44:59 +02:00
ikeller	0e3898eabf	modify singularity settings	2021-05-20 10:53:35 +02:00
MaxUlysse	05548bdb75	fix: forgotten }	2021-05-20 09:37:48 +02:00
Olga Botvinnik	8166e0f606	executor.cli --> aws.batch.cliPath	2021-05-19 13:36:15 -07:00
MaxUlysse	73fcc4495a	feat: update owner of profile	2021-05-19 20:46:52 +02:00
Asaf Peer	82fadc7061	replaced owner in JAX	2021-05-19 13:48:49 -04:00
Phil Ewels	9c4830c8d5	Merge pull request #238 from nf-core/hebbe-config-fix	2021-05-19 17:46:52 +02:00
ikeller	af1e57027d	edit config and readme	2021-05-19 09:46:07 +02:00
ikeller	fb3cede5d3	add config file	2021-05-19 08:41:55 +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
Maxime U. Garcia	77bd7f567f	Merge pull request #228 from asafpr/master ... updated jax resources	2021-05-02 14:47:19 +02:00
Phil Ewels	76b62b478d	Fix hebbe withName regex	2021-04-29 23:06:56 +02:00
Barry digby	24a4119e43	memory test	2021-04-29 14:24:57 +01:00
Barry digby	aeb0346cce	.	2021-04-28 20:14:32 +01:00
Barry digby	8340e89768	nuig.config first commit	2021-04-28 17:28:01 +01:00
Alexander Peltzer	c12c373969	Merge pull request #235 from aunderwo/cambridge ... Add Cambridge University HPC config	2021-04-25 10:40:56 +02:00
Gisela Gabernet	4e9e5d2c67	Merge branch 'master' into cfc_sarek	2021-04-23 16:47:04 +02:00
Anthony Underwood	8b3951b244	Create cambridge.config	2021-04-22 16:00:37 +01:00
Anthony Underwood	351c5773f0	Add queue limits for 'normal'	2021-04-22 11:59:34 +01:00
Anthony Underwood	7d8770af1a	Create sanger.config	2021-04-21 16:39:55 +01:00
phue	b225a0555a	biohpc_gen: update software tree path	2021-04-21 10:08:00 +02:00
James A. Fellows Yates	eacdf89e53	Update eva.config	2021-04-20 13:17:35 +02:00
James A. Fellows Yates	b9a00f7926	Update mpcdf.config	2021-04-15 22:27:07 +02:00
Harshil Patel	7ac66dcd72	Update crick.config	2021-04-13 17:07:02 +01:00
Combiz Khozoie	c571c05ab9	Merge pull request #219 from slacalle/patch-2 ... Imperial College | Remove "/rdsgpfs"	2021-04-13 15:28:00 +01:00
MaxUlysse	3918e0aa9d	feat: remove kraken profile	2021-04-13 15:14:14 +02:00
Asaf Peer	a0c8a9ec8f	updated jax resources	2021-04-12 16:00:34 -04:00
Pontus Freyhult	ff20f121f9	Support use of very fat node in snowy	2021-04-12 19:34:28 +02:00
Pontus Freyhult	0987cbe1be	Better test for snowy	2021-04-12 19:32:21 +02:00
Pontus Freyhult	7be4279718	Handle different (unexpected) sinfo returns in different cases	2021-04-12 19:31:41 +02:00
Pontus Freyhult	57c26c13d9	Redo cases for simplification	2021-04-12 19:21:58 +02:00
Phil Ewels	2f77d16b70	Merge pull request #220 from ewels/master ... UPPMAX: Avoid undefined parameter warnings	2021-04-08 15:06:00 +02:00
Pontus Freyhult	be6ea0060f	Wrap sinfo call in a try/catch and default to rackham on failure	2021-04-08 09:49:42 +02:00
Pontus Freyhult	fa1b4cb412	Move cluster options creating closure out of process scope	2021-04-08 09:45:29 +02:00
James A. Fellows Yates	161c3a33d4	Merge branch 'master' into eva	2021-04-07 19:28:16 +02:00
James A. Fellows Yates	ce465cca57	Apply suggestions from code review ... Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>	2021-04-07 19:27:24 +02:00
Pontus Freyhult	4d64db85eb	Determine cluster through slurm	2021-04-07 18:43:32 +02:00
Pontus Freyhult	c5070f3eba	Use node queue when more memory than thin nodes have	2021-04-07 18:43:32 +02:00
Alexander Peltzer	91f50aad4e	Merge pull request #221 from phue/biohpc_gen ... Add BioHPC Genomics config	2021-04-07 14:03:22 +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
phue	60ae267e43	use SLURM_CLUSTERS env var ... this seems to be more reliable for queue checking than using the clusterOptions directive. See https://github.com/nextflow-io/nextflow/issues/807	2021-04-06 11:35:01 +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
phue	8fc60e2e70	add config for biohpc_gen	2021-03-29 19:25:58 +02:00
Gisela Gabernet	71a97ba316	Merge pull request #185 from ggabernet/master ... awsbatch config update	2021-03-28 20:59:40 +02:00
Phil Ewels	d34bc40841	UPPMAX: add to schema_ignore_params	2021-03-26 15:22:57 +01:00
Phil Ewels	eccc9ea8d5	Define params.project and params.clusterOptions in uppmax config	2021-03-26 15:20:32 +01:00
Santiago Lacalle	e2c583d558	Remove "/rdsgpfs" ... "/rdsgpfs" symlink will not be present on all nodes. Without that mount the container creation will fail.	2021-03-25 12:38:15 +00:00
Alexander Peltzer	26b5904df1	Merge pull request #218 from asafpr/master ... added jax singularity cache dir	2021-03-24 17:39:03 +01:00
Asaf Peer	922ab87eb0	added jax singularity cache dir	2021-03-24 11:25:47 -04:00
Phil Ewels	bfab371c94	Merge branch 'master' into master	2021-03-24 12:36:15 +01:00
ameyner2	da8cf2f207	Added pipeline-specific config files for rnaseq and sarek	2021-03-24 10:46:26 +00:00
Asaf Peer	9b2d5bfead	Merge pull request #216 from asafpr/master ... Added JAX conf	2021-03-24 03:31:14 -04:00
Alexander Peltzer	5988c51361	Merge pull request #211 from DoaneAS/master ... Adding WCM.config for Weill Cornell Medicine cluster	2021-03-23 14:58:27 +01:00
Edmund Miller	a6975cdd4e	fix(ganymede): large => high ... Co-authored-by: drpatelh <drpatelh@users.noreply.github.com>	2021-03-22 12:42:56 -05:00
Edmund Miller	34ccce9531	fix(ganymede): Add process resources ... Trimgalore though it can be a bottom neck, doesn't require the 1 big memory node we have and can be run on the genomics queue.	2021-03-21 21:47:59 -05:00
Edmund Miller	4570718b12	fix(ganymede): Add TMPDIR and SINGULARITY_CACHEDIR env variables	2021-03-21 21:45:39 -05:00
Asaf Peer	30c864e112	added JAX conf	2021-03-21 06:49:11 -04:00
ameyner2	059d353a1e	Removed Conda, added automount Singularity	2021-03-18 12:31:56 +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
ameyner2	d4cd07c646	Typo in beforescript	2021-03-17 09:21:26 +00:00
Noirot Céline	7e9f83ee81	Add IFB config	2021-03-16 15:54:19 +01:00
ameyner2	cfe13fe6c1	Fixed typo & added singularity tmpdir	2021-03-15 15:42:30 +00:00
Ashley S Doane	e7f8189dfc	Create wcm.config	2021-03-11 13:52:11 -05:00
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
phue	da3bd2693d	cbe: add rapid qos ... and update config url	2021-03-10 11:26:01 +01:00
FriederikeHanssen	eb9012919c	Set values for processes with max_mem/max_cpus	2021-03-10 11:16:18 +01:00
Graeme Grimes	babeccd020	changed # to // for comments	2021-03-04 16:45:21 +00:00
ameynert	6f09a233f0	Added singularity module	2021-03-04 14:46:23 +00:00
ameynert	3af2c6409f	Initial commit of eddie.config	2021-03-03 09:59:16 +00:00
maxibor	286e18b80c	update shh config after CDAG departure	2021-02-17 10:22:05 +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
Marc Hoeppner	1f2fce00aa	Updating the CCGA DX profile to new storage system	2021-02-16 09:02:16 +01:00
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
ggabernet	9b5bcbd434	update aws clipath	2021-02-09 22:06:59 +01:00
ggabernet	0909708b97	update with upstream	2021-02-09 22:01:27 +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
Charles Plessy	1608b36dcf	Institutional profile for Okinawa Institute of Science and Technology	2021-02-02 17:40:10 +09:00
Thiseas C. Lamnidis	713a032a36	Add debug profile ... which deactivates cleanup of workdir after successful run	2021-01-26 15:08:21 +01:00
James A. Fellows Yates	26d164ca74	Remove ceh profile for now	2021-01-21 13:15:08 +01:00
Åshild J. Vågene	594985f1ee	Update and rename ceh.config to seg_globe.config	2021-01-21 11:43:34 +01:00
Åshild J. Vågene	8fa720b9cc	Update conf/ceh.config ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2021-01-21 11:15:06 +01:00
Åshild J. Vågene	f8973f153a	Update ceh.config	2021-01-21 00:31:49 +01:00
Åshild J. Vågene	91594dffea	Update ceh.config	2021-01-21 00:29:43 +01:00
Åshild J. Vågene	c11c26f15f	Create ceh.config	2021-01-20 23:45:26 +01:00
James A. Fellows Yates	1c25cb033b	Add big_data profile	2021-01-19 13:53:01 +01:00
rbpisupati	9b5ac5c89d	added anaconda module for cbe	2021-01-15 12:55:46 +01:00
James A. Fellows Yates	a4c55b3ea9	Fix time limit 0-9 typo	2021-01-06 10:44:12 +01:00
Combiz Khozoie	17cf4e3b35	fixed indents	2020-12-18 15:34:56 +00:00
Combiz Khozoie	3824403b4e	removed workDir from Imperial configs	2020-12-18 10:31:36 +00:00
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
marcel-keller	c9ceaff3b3	change of directory for conda environments ... change of directory due to recent changes in our infrastructure	2020-12-09 15:11:21 +02:00
emnilsson	8cc2fc5ecb	Merge pull request #193 from emnilsson/master ... Modified ampliseq-specific uppmax-config	2020-12-02 13:40:43 +01:00
Alexander Peltzer	99985c658f	Merge pull request #194 from marcel-keller/ebc ... Update ebc.config	2020-11-26 14:12:33 +01:00
marcel-keller	5590a9743a	Update ebc.config ... queueSize to 64	2020-11-26 15:05:25 +02:00
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	cd59bba83e	Merge branch 'master' of https://github.com/nf-core/configs	2020-11-24 07:10:05 +01:00
Emelie Nilsso	c47088cda2	Merge remote-tracking branch 'origin'	2020-11-23 21:34:08 +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
Thiseas C. Lamnidis	71d1ff2226	Add params block to sdag queue ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2020-11-18 13:04:46 +01:00
Thiseas C. Lamnidis	da781907f2	Move sdag queue specification block in sdag profile	2020-11-17 19:45:06 +01:00
Maxime Borry	c95fd9d52f	Merge pull request #186 from jfy133/shh-singularity-runoptions ... Remove custom singularity runOptions from SHH config	2020-11-10 15:39:40 +01:00
James A. Fellows Yates	9d4d682867	Update shh.config	2020-11-10 15:14:03 +01:00
Gisela Gabernet Garriga	885f0ce5f6	awsbatch config update	2020-11-09 22:41:38 +01:00
lecorguille	90d1f9072b	Add ABiMS - autoMounts = false	2020-10-22 18:18:55 +02:00
lecorguille	a63ca751ee	Add ABiMS	2020-10-22 16:57:41 +02:00
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
James A. Fellows Yates	3995057d7f	Update mpcdf.config	2020-10-22 10:42:46 +02:00
James A. Fellows Yates	05deeca2d6	Update mpcdf.config	2020-10-15 14:22:35 +02:00
James A. Fellows Yates	e26c22b2f1	Update shh.config	2020-09-29 14:03:35 +02:00
MaxUlysse	2ccbdd3367	update params to latest version	2020-09-28 13:59:42 +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	bbbdd3cb0f	Update mpcdf.config	2020-09-16 10:21:42 +02:00
James A. Fellows Yates	5b3492d240	Update mpcdf.config	2020-09-16 10:21:26 +02:00
James A. Fellows Yates	3115963b3e	Update mpcdf.config	2020-09-15 19:53:27 +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
Edmund Miller	2c06019d89	fix(utd): Add check for less than 12 cpu	2020-09-13 20:46:14 -05:00
Edmund Miller	dc2735207e	feat(utd): add Kim queue	2020-09-13 20:46:10 -05:00
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
James A. Fellows Yates	b4e275c3b9	Add MPCDF for EAGER	2020-09-04 19:57:25 +02:00
James A. Fellows Yates	5c7ab234b6	Create mpcdf.config	2020-09-04 19:55:40 +02:00
James A. Fellows Yates	0a685c1cc2	Update mpcdf.config	2020-09-03 20:24:11 +02:00
James A. Fellows Yates	42a1a15970	Create mpcdf.config	2020-09-03 20:11:56 +02:00
James A. Fellows Yates	c3fa87e4bc	Add microbiome screening profile for NT sized MALT runs for nf-core/eager@SHH	2020-08-11 09:18:36 +02:00
drpatelh	b804076959	Remove hard Singularity version	2020-08-03 11:38:10 +01:00
maxibor	69a0bd572b	add temporary CDAG setting for SHH config	2020-07-23 15:38:28 +02:00
James A. Fellows Yates	d38ffc289b	Merge pull request #173 from jfy133/shh-eager-hops-update ... Remove now deprecated EAGER flag for HOPS profile	2020-07-20 11:34:49 +02:00
James A. Fellows Yates	57ac9257a9	Remove now deprecated EAGER flag for HOPS profile	2020-07-20 11:29:12 +02:00
Alexander Peltzer	a498e98342	Merge pull request #170 from jfy133/master ... Make walltimes more sophisticated and add a HOPS profile for nf-core/eager @ SHH	2020-07-15 15:11:24 +02:00
James A. Fellows Yates	84e03b8264	Re-bump default walltimes after debugging/testing	2020-07-11 18:31:04 +02:00
James A. Fellows Yates	8f6409d144	Remove min support percent value to avoid confusion	2020-07-08 15:26:19 +02:00
James A. Fellows Yates	1af9ce293c	Update hops profile based on requests from pathogen group	2020-07-08 15:22:33 +02:00
James A. Fellows Yates	c57a404f18	Add desc for hops	2020-07-08 10:45:43 +02:00
jfy133	15dad7e2e7	Add caveats for EAGER @ SHH profiles	2020-07-08 09:47:03 +02:00
jfy133	926c14f7ee	Cleverer process time submission	2020-07-08 09:36:56 +02:00
jfy133	563c27e1bb	Try again to get better time resource submission	2020-07-08 09:36:28 +02:00
James A. Fellows Yates	c6905b609e	Update shh.config	2020-07-08 09:25:21 +02:00
James A. Fellows Yates	b360ce26bc	Update shh.config	2020-07-08 09:24:06 +02:00
James A. Fellows Yates	31edb4b5d7	Update shh.config	2020-07-08 09:20:00 +02:00
James A. Fellows Yates	aac3478e86	Add better task time values to account for large data	2020-07-08 09:12:11 +02:00
James A. Fellows Yates	737d826932	Update shh.config	2020-07-08 08:36:04 +02:00
piotr-faba-ardigen	ba24f1a1c8	Merge pull request #168 from piotr-faba-ardigen/add_bi_config ... Fix bi config	2020-07-07 14:56:43 +02:00
James A. Fellows Yates	fcdbeaa446	Merge branch 'master' into master	2020-07-07 14:34:10 +02:00
James A. Fellows Yates	af01fccba1	Add a HOPS profile for nf-core/eager @ SHH	2020-07-07 14:31:11 +02:00
Piotr Faba	cb7a6f756a	reduce complexity	2020-07-07 13:48:28 +02:00
James A. Fellows Yates	5517d2cbe0	Remove default non-profile bwa parameters from eager profile ... I realised today this is dangerous as these would not necessarily be reported if a user doesn't understand the profiles. Therefore removing these so nf-core/eager defaults are always used unless a specific profile (which would be described in the command itself) is explicitly named.	2020-07-07 13:29:13 +02:00
Piotr Faba	4181184f58	fix spaces	2020-07-02 22:00:37 +02:00
Piotr Faba	4828e78708	fix error introduced earlier	2020-07-02 21:57:44 +02:00
James A. Fellows Yates	530da4d8c0	Merge pull request #167 from jfy133/master ... Bump number of eager @shh retries to account for deep sequencing data	2020-06-30 11:33:29 +02:00
James A. Fellows Yates	c52428cd72	Bump number of eager @shh retries to account for deep sequencing data	2020-06-30 08:19:25 +02:00
Adrian	e375ad97ad	reverting autoMounts due to bug	2020-06-26 13:39:37 +01:00
Phil Ewels	28027a8489	Prince config - use function to check if env SCRATCH is set	2020-06-26 14:22:32 +02:00
Phil Ewels	cd9fbb22dc	Merge pull request #161 from ewels/uct_hpc ... Update UCT hex -> hpc	2020-06-22 09:18:43 +02:00
Alexander Peltzer	7774a6a8f3	Merge pull request #163 from piotr-faba-ardigen/add_bi_config ... resolve #162 bug	2020-06-19 08:57:44 +02:00
Piotr Faba	cb26bef3f3	resolve #162 bug	2020-06-18 20:30:05 +02:00
Phil Ewels	53e118210f	Copy over HPC config	2020-06-17 15:20:22 +02:00
Phil Ewels	dbfcd7c5e9	Rename uct_hex > uct_hpc	2020-06-17 15:17:22 +02:00
Phil Ewels	17824d2d62	Merge czbiohub_aws_highpriority profile into czbiohub_aws	2020-06-16 15:20:39 +02:00
phue	6d356cc918	CBE: don't load singularity module ... singularity is now installed from CentOS repos, the environment module will be removed	2020-06-05 12:07:26 +02:00
Alexander Peltzer	f877644059	Merge branch 'master' into master	2020-05-29 11:43:47 +02:00
Alexander Peltzer	32ec230098	Merge pull request #156 from piotr-faba-ardigen/add_bi_config ... Add bi config	2020-05-27 21:03:15 +02:00
Piotr Faba	f139750bf4	print the error message before throwing Exception	2020-05-27 19:14:43 +02:00
Piotr Faba	3c695ba71c	test error display	2020-05-27 18:00:47 +02:00
Alexander Peltzer	6011419454	Merge pull request #154 from jfy133/master ... Update SHH nf-core/eager group-specific profiles	2020-05-27 17:52:09 +02:00
Piotr Faba	18d8edb046	add description and profile	2020-05-27 17:41:19 +02:00
Piotr Faba	66f191a1cf	declate NXF_GLOBAL_CONFIG in ci	2020-05-27 16:30:00 +02:00
Piotr Faba	2685275952	switch include off	2020-05-27 16:24:47 +02:00
Piotr Faba	c31b03108c	retry without Exception	2020-05-27 16:22:56 +02:00
Piotr Faba	1354ae4063	add bi config	2020-05-27 16:19:15 +02:00
James A. Fellows Yates	d070ed70d1	Update BWA settings based on feedback	2020-05-26 11:11:42 +02:00
James A. Fellows Yates	e31e781f29	Remove debugging	2020-05-26 11:07:06 +02:00
Harshil Patel	5981e5ec27	Merge pull request #153 from FriederikeHanssen/cfc_scratch ... Add scratch = true to avoid writing of intermediate file to /tmp	2020-05-22 15:48:00 +01:00
James A. Fellows Yates	ff915ee504	Update shh.config	2020-05-12 12:47:59 +02:00
James A. Fellows Yates	8225e07819	Condensed base params and added names for debugging	2020-05-12 12:47:25 +02:00
James A. Fellows Yates	4814bac1c3	Fix sub-profiles	2020-05-12 12:42:42 +02:00
James A. Fellows Yates	38e9e54932	Merge pull request #151 from jfy133/master ... Add additional custom nf-core/eager params for SHH profile	2020-05-07 09:25:02 +02:00
James A. Fellows Yates	cf6e697f0b	Further update aln based on modifications of EAGER defaults	2020-05-07 09:16:08 +02:00
James A. Fellows Yates	d42d7f4146	Sets the bwa aln parameter to 0.01 which is more commonly used at SHH	2020-05-04 21:02:16 +02:00
FriederikeHanssen	d6813d9c39	Add scratch = true to avoid writing of intermediate file to /tmp	2020-05-04 17:09:43 +02:00
MaxUlysse	e6f4d58fa6	update rnafusion munin specific config	2020-04-28 17:06:04 +02:00
Adrian	ad12bd4ad1	testing automounts	2020-04-28 16:03:06 +01:00
Harshil Patel	2300d5a962	Update genomes.config	2020-04-09 18:22:41 +01:00
MaxUlysse	50a44d037b	better docs and organisation of giles	2020-04-09 17:02:36 +02:00
Maxime Garcia	34dc18faf6	Update uppmax.config	2020-04-09 11:35:37 +02:00
Adrian Larkeryd	405801638a	icr_davros sarek config description	2020-04-08 11:56:17 +01:00
Adrian Larkeryd	78be4b358e	icr_davros igenomes base	2020-04-08 11:55:16 +01:00
Maxime Garcia	d1ff87a416	Merge pull request #145 from bioatlas/master ... Adding UPPMAX specific config for ampliseq	2020-03-31 15:46:21 +02:00
Daniel Lundin	c8de9be701	Adding UPPMAX specific config for ampliseq	2020-03-31 15:17:24 +02:00
MaxUlysse	db2dd4458b	Merge remote-tracking branch 'upstream/master' into UPPMAX	2020-03-30 16:41:08 +02:00
MaxUlysse	8b570507cd	update s	2020-03-30 16:40:11 +02:00
ggabernet	c81f693f73	add cfc_dev config	2020-03-23 17:16:34 +01:00
Olga Botvinnik	52369ba6ad	Add AaegL5.0 config	2020-03-17 16:45:20 -07:00
Maxime Garcia	123132d89a	Update munin.config ... fix typo	2020-03-12 17:23:55 +01:00
Phil Ewels	5a3bdcca5b	Merge pull request #139 from Emiller88/utd ... fix(ganymede): use singularity/2.4.5	2020-03-11 16:54:01 +00:00
Maxime Garcia	b6d52fdb89	Update conf/pipeline/sarek/munin.config	2020-03-11 15:48:29 +01:00
Maxime Garcia	0f34d757a9	Update munin.config	2020-03-11 15:48:17 +01:00
MaxUlysse	d24a296a01	add munin/rnafusion specific config	2020-03-11 14:02:01 +01:00
MaxUlysse	dd1ddf864b	update sarek munin config	2020-03-11 14:01:28 +01:00
Edmund Miller	cece853663	fix(ganymede): use singularity/2.4.5 ... Our 3.2.1 doesn't work right with snakemake or nextflow	2020-03-10 21:03:24 -05:00
Edmund Miller	c42bb07981	fix: Singularity => singularity ... For some reason ours are lowercase	2020-03-10 09:55:17 -05:00
Edmund Miller	123c44c56d	feat: add initial ganymede config	2020-03-09 16:18:41 -05:00
marcel-keller	8e3803e4d7	Update ebc.config	2020-03-09 16:57:45 +02:00
marcel-keller	c00bbe982b	Update ebc.config	2020-03-09 16:51:38 +02:00
marcel-keller	3b57519500	Update ebc.config	2020-03-09 16:48:50 +02:00
marcel-keller	de914e56ee	Create ebc.config	2020-03-09 16:08:01 +02:00
Evan Floden	d8ad376f71	Merge branch 'master' into master	2020-03-06 10:29:50 +00:00
Alexander Peltzer	59a787b179	Merge pull request #122 from marchoeppner/ccga-config ... Removing old CCGA profile from docs and linting	2020-03-06 11:17:08 +01:00
mseybold	52842de88b	Update cfc.config ... test failed, so added the the default queue	2020-03-06 10:46:37 +01:00
mseybold	8e42bbd7d0	Update cfc.config ... We just added some new HighMem nodes to the cfc, Partition/queue name is qbic, each node has 128Cores and 2TB of RAM. The old queue (Name compute) is set to default by slurm. Each process over 60GB of RAM or over 20cpus should run on those new nodes. So added the queue State and adjusted the max_memory and max_cpu setting.	2020-03-06 10:25:08 +01:00
Evan Floden	8a9d3ad8a0	First commit of Google Cloud config	2020-03-06 05:47:29 +00:00
phue	e2e4dd05d3	cbe: move container cache to different filesystem ... this is a workaround for squashfs errors that occur when containers are run from beeGFS	2020-03-05 16:34:20 +01:00
Adrian Larkeryd	a67e77bb57	put comments back in correct format	2020-03-05 10:42:18 +00:00
Adrian Larkeryd	46223a3dbb	remove comments	2020-03-05 10:39:19 +00:00
Adrian Larkeryd	ead67d1e90	description and contact	2020-03-05 09:24:10 +00:00
Adrian Larkeryd	a882b6cbaa	adding icr_davros config files generic and sarek	2020-03-04 15:00:33 +00:00
James A. Fellows Yates	41a45187fa	Experiment to see if 'cleanup = true' works as expected	2020-03-03 16:47:49 +01:00
Maxime Garcia	9a8bb12020	Update conf/pipeline/sarek/uppmax.config	2020-02-27 17:22:03 +01:00
Maxime Garcia	8acbdacf03	Update conf/pipeline/sarek/uppmax.config ... Co-Authored-By: Johannes Alneberg <johannes.alneberg@scilifelab.se>	2020-02-27 17:21:03 +01:00
Maxime Garcia	09ff8f5790	Update conf/pipeline/sarek/uppmax.config	2020-02-27 17:02:31 +01:00
Maxime Garcia	17d6a7e922	Update conf/pipeline/sarek/uppmax.config	2020-02-27 17:02:13 +01:00
Maxime Garcia	ab8998e12b	Update uppmax.config	2020-02-27 16:52:51 +01:00
MaxUlysse	a8d338d2aa	Merge branch 'Uppmax' of github.com:MaxUlysse/nf-core_configs into Uppmax	2020-02-24 14:37:27 +01:00
MaxUlysse	9f74e88041	update file	2020-02-24 14:36:45 +01:00
Marc Hoeppner	6c5a5c8bcb	Removing old CCGA profile from docs and linting ... Removing CCGA profile from master config Removing CCGA profile from master config	2020-02-24 12:16:33 +01:00
Maxime Garcia	9b897345da	Update conf/pipeline/sarek/uppmax.config ... Co-Authored-By: Phil Ewels <phil.ewels@scilifelab.se>	2020-02-21 08:16:31 +01:00
Maxime Garcia	08e2804b37	Merge branch 'master' into Uppmax	2020-02-20 17:18:46 +01:00
MaxUlysse	aa905cd645	add UPPMAX specific sarek config	2020-02-20 17:14:18 +01:00
Daniel Straub	744db30da4	Update binac.config ... This is now close to optimal I think.	2020-02-19 11:27:02 +01:00
marchoeppner	0830203b70	Adding new CCGA Med Cluster to profiles ... Updating README and fixing linting errors in CCGA_MED profile Fixing order in profile queue and removed leading slash from readme for ccga profile docs Fixing order in profile queue and removed leading slash from readme for ccga profile docs	2020-02-11 11:12:51 +01:00
Daniel Straub	b7be65a31e	Cleanup config	2020-02-07 14:53:43 +01:00
Daniel Straub	7346bffdc8	Update binac.config ... Processes that ask for 128 Gb are queuing forever when on short queue, but executed when send to smp queue.	2020-01-28 08:48:34 +01:00
James A. Fellows Yates	638758423a	Restricts MALT re-tries and hardcodes resources so cannot go above SDAG max	2019-12-21 20:55:54 +01:00
drpatelh	67c231d05c	Change igenomes path	2019-12-18 10:54:23 +00:00
drpatelh	089b5b8e3b	Update config	2019-12-12 13:44:37 +00:00
drpatelh	65c5668568	Update config	2019-12-12 13:02:44 +00:00
Maxime Garcia	d36172d4cf	Merge pull request #110 from MaxUlysse/MUNIN ... fix issue with withLabel selector	2019-12-12 13:03:23 +01:00
MaxUlysse	2bf66514c5	fix issue with withLabel selector	2019-12-12 11:50:10 +01:00
Alexander Peltzer	a6d08ed646	Adjust custom pipeline config for ampliseq on BINAC	2019-12-11 16:09:44 +01:00
Alexander Peltzer	49cd35918a	Remove whitespace	2019-12-11 15:59:58 +01:00
Alexander Peltzer	5e6981d0ee	Export TZ in binac config	2019-12-11 15:59:25 +01:00
Alexander Peltzer	ac90acf470	Update envWhiteList for Binac Profile for testing purposes ... Add envWhitelist for TZ to fix https://github.com/nf-core/ampliseq/issues/114	2019-12-11 14:26:57 +01:00
James A. Fellows Yates	0beb98696f	Merge branch 'master' into master	2019-12-06 19:31:24 +01:00
James A. Fellows Yates	8747be8120	More tweaks, nextflow appears to add a little extra?	2019-12-06 19:27:16 +01:00
James A. Fellows Yates	5c6760b2f0	Tweak back again	2019-12-06 19:25:07 +01:00
James A. Fellows Yates	46f6d20a77	Put parameters back to correct levels	2019-12-06 19:13:29 +01:00
James A. Fellows Yates	18931763fa	Add space?	2019-12-06 19:11:08 +01:00
James A. Fellows Yates	f59443daf0	Update shh.config	2019-12-06 19:09:20 +01:00
James A. Fellows Yates	1ab1370872	Try to make resources satisfiable	2019-12-06 19:06:05 +01:00
James A. Fellows Yates	6e596d1730	Fix stupid wrong bracket typo -.-	2019-12-06 18:37:39 +01:00