1372 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
Phil Ewels	2afb4f0ad6	Don't recommend setting --custom_config_base manually	2021-04-13 14:37:54 +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	095cd483e6	Update README.md	2021-04-07 20:43:31 +02:00
James A. Fellows Yates	033f81734a	Make a bit more explicitly exactly what you have to add/update	2021-04-07 20:32:44 +02:00
James A. Fellows Yates	beae329b29	Add docs as to what exactly you have to do when adding new config	2021-04-07 20:24:55 +02:00
James A. Fellows Yates	a2a47fdecc	Merge pull request #224 from jfy133/eva ... Add EVA profile for MPI-EVA (clean)	2021-04-07 19:56:00 +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
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
Patrick Hüther	53b54ba845	Remove whitespace ... Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>	2021-04-07 13:18:06 +02:00
ameynert	efa051b3e4	Merge pull request #222 from ameynert/master ... Addition of ATAC-seq pipeline config, updated docs	2021-04-07 09:48:29 +01:00
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 Fellows Yates	8dac4ca552	Merge branch 'eva' of github.com:jfy133/configs into eva	2021-04-06 17:53:32 +02:00
James Fellows Yates	60c66d93ac	Markdown linting	2021-04-06 17:53:27 +02:00
James A. Fellows Yates	832edaa450	Merge branch 'master' into eva	2021-04-06 17:51:46 +02:00
James A. Fellows Yates	504c10d6ff	Update README.md	2021-04-06 17:50:25 +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
ameynert	700776f759	Change to shared Singularity cache	2021-03-30 16:11:15 +01:00
ameynert	25716fe849	Merge pull request #2 from nf-core/master ... Merge commits from nf-core/configs master	2021-03-30 16:09:32 +01:00
phue	7c5a0871a3	add note about required nextflow version	2021-03-29 19:36:49 +02:00
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
ameynert	6215414ecf	Merge pull request #217 from ameynert/master ... Addition of eddie institutional profile	2021-03-24 14:05:07 +00:00
ameynert	3a8e54f153	Removed sneaky trailing whitespace.	2021-03-24 13:58:10 +00:00
ameynert	a0d42f5153	Fixed code blocks for markdown linting	2021-03-24 13:55:31 +00:00
ameynert	2d90c919aa	Added eddie profile to github workflow tests	2021-03-24 13:51:37 +00:00
Phil Ewels	8e6223d1bd	Update nfcore_custom.config	2021-03-24 12:36:50 +01:00
Phil Ewels	bfab371c94	Merge branch 'master' into master	2021-03-24 12:36:15 +01:00
Phil Ewels	158402eddf	Update nfcore_custom.config	2021-03-24 12:26:49 +01:00
ameynert	aeb0ffcfde	Spacing fix ... Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>	2021-03-24 11:26:09 +00:00
ameynert	2a8ae2b214	Update eddie.md	2021-03-24 11:12:41 +00:00