531 commits

Author	SHA1	Message	Date
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
Phil Ewels	2f77d16b70	Merge pull request #220 from ewels/master ... UPPMAX: Avoid undefined parameter warnings	2021-04-08 15:06:00 +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
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	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