Phil Ewels
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2afb4f0ad6
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Don't recommend setting --custom_config_base manually
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2021-04-13 14:37:54 +02:00 |
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Asaf Peer
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a0c8a9ec8f
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updated jax resources
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2021-04-12 16:00:34 -04:00 |
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Pontus Freyhult
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ff20f121f9
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Support use of very fat node in snowy
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2021-04-12 19:34:28 +02:00 |
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Pontus Freyhult
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0987cbe1be
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Better test for snowy
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2021-04-12 19:32:21 +02:00 |
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Pontus Freyhult
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7be4279718
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Handle different (unexpected) sinfo returns in different cases
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2021-04-12 19:31:41 +02:00 |
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Pontus Freyhult
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57c26c13d9
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Redo cases for simplification
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2021-04-12 19:21:58 +02:00 |
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Phil Ewels
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2f77d16b70
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Merge pull request #220 from ewels/master
UPPMAX: Avoid undefined parameter warnings
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2021-04-08 15:06:00 +02:00 |
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Pontus Freyhult
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be6ea0060f
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Wrap sinfo call in a try/catch and default to rackham on failure
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2021-04-08 09:49:42 +02:00 |
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Pontus Freyhult
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fa1b4cb412
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Move cluster options creating closure out of process scope
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2021-04-08 09:45:29 +02:00 |
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James A. Fellows Yates
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a2a47fdecc
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Merge pull request #224 from jfy133/eva
Add EVA profile for MPI-EVA (clean)
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2021-04-07 19:56:00 +02:00 |
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James A. Fellows Yates
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161c3a33d4
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Merge branch 'master' into eva
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2021-04-07 19:28:16 +02:00 |
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James A. Fellows Yates
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ce465cca57
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Apply suggestions from code review
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
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2021-04-07 19:27:24 +02:00 |
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Pontus Freyhult
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4d64db85eb
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Determine cluster through slurm
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2021-04-07 18:43:32 +02:00 |
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Pontus Freyhult
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c5070f3eba
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Use node queue when more memory than thin nodes have
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2021-04-07 18:43:32 +02:00 |
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Alexander Peltzer
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91f50aad4e
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Merge pull request #221 from phue/biohpc_gen
Add BioHPC Genomics config
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2021-04-07 14:03:22 +02:00 |
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Patrick Hüther
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53b54ba845
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Remove whitespace
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
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2021-04-07 13:18:06 +02:00 |
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ameynert
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efa051b3e4
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Merge pull request #222 from ameynert/master
Addition of ATAC-seq pipeline config, updated docs
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2021-04-07 09:48:29 +01:00 |
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ameynert
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0ab9edde72
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Delete conf/pipeline/atacseq directory
Pipeline-specific config not supported yet by ATAC-seq pipeline
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2021-04-07 09:24:30 +01:00 |
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James Fellows Yates
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8dac4ca552
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Merge branch 'eva' of github.com:jfy133/configs into eva
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2021-04-06 17:53:32 +02:00 |
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James Fellows Yates
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60c66d93ac
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Markdown linting
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2021-04-06 17:53:27 +02:00 |
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James A. Fellows Yates
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832edaa450
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Merge branch 'master' into eva
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2021-04-06 17:51:46 +02:00 |
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James A. Fellows Yates
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504c10d6ff
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Update README.md
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2021-04-06 17:50:25 +02:00 |
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James Fellows Yates
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be1d35840d
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Add EVA and EAGER@EVA
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2021-04-06 17:48:16 +02:00 |
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James Fellows Yates
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d69af0f287
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Merging
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2021-04-06 16:42:22 +02:00 |
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phue
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60ae267e43
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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
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2021-04-06 11:35:01 +02:00 |
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ameynert
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6e201a71f4
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ATAC-seq pipeline config
Java processes with overhead memory requirements
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2021-03-30 16:31:00 +01:00 |
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ameynert
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e5f2a63079
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Java overhead processes list updated
Added all processes calling GATK for Mutect2 variant calling
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2021-03-30 16:21:53 +01:00 |
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ameynert
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adfb5366b9
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Java overhead process list updated
Added HaplotypeCaller and GenotypeGVCFs to set of processes that need Java overhead
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2021-03-30 16:15:17 +01:00 |
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ameynert
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700776f759
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Change to shared Singularity cache
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2021-03-30 16:11:15 +01:00 |
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ameynert
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25716fe849
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Merge pull request #2 from nf-core/master
Merge commits from nf-core/configs master
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2021-03-30 16:09:32 +01:00 |
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phue
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7c5a0871a3
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add note about required nextflow version
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2021-03-29 19:36:49 +02:00 |
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phue
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8fc60e2e70
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add config for biohpc_gen
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2021-03-29 19:25:58 +02:00 |
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Gisela Gabernet
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71a97ba316
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Merge pull request #185 from ggabernet/master
awsbatch config update
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2021-03-28 20:59:40 +02:00 |
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Phil Ewels
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d34bc40841
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UPPMAX: add to schema_ignore_params
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2021-03-26 15:22:57 +01:00 |
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Phil Ewels
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eccc9ea8d5
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Define params.project and params.clusterOptions in uppmax config
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2021-03-26 15:20:32 +01:00 |
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Santiago Lacalle
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e2c583d558
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Remove "/rdsgpfs"
"/rdsgpfs" symlink will not be present on all nodes. Without that mount the container creation will fail.
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2021-03-25 12:38:15 +00:00 |
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Alexander Peltzer
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26b5904df1
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Merge pull request #218 from asafpr/master
added jax singularity cache dir
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2021-03-24 17:39:03 +01:00 |
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Asaf Peer
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922ab87eb0
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added jax singularity cache dir
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2021-03-24 11:25:47 -04:00 |
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ameynert
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6215414ecf
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Merge pull request #217 from ameynert/master
Addition of eddie institutional profile
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2021-03-24 14:05:07 +00:00 |
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ameynert
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3a8e54f153
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Removed sneaky trailing whitespace.
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2021-03-24 13:58:10 +00:00 |
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ameynert
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a0d42f5153
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Fixed code blocks for markdown linting
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2021-03-24 13:55:31 +00:00 |
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ameynert
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2d90c919aa
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Added eddie profile to github workflow tests
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2021-03-24 13:51:37 +00:00 |
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Phil Ewels
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8e6223d1bd
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Update nfcore_custom.config
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2021-03-24 12:36:50 +01:00 |
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Phil Ewels
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bfab371c94
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Merge branch 'master' into master
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2021-03-24 12:36:15 +01:00 |
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Phil Ewels
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158402eddf
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Update nfcore_custom.config
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2021-03-24 12:26:49 +01:00 |
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ameynert
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aeb0ffcfde
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Spacing fix
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
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2021-03-24 11:26:09 +00:00 |
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ameynert
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2a8ae2b214
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Update eddie.md
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2021-03-24 11:12:41 +00:00 |
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ameynert
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96fe6185a0
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IGMM-specific docs
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2021-03-24 11:01:41 +00:00 |
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ameyner2
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00d984d918
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Merge branch 'master' of github.com:ameynert/configs
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2021-03-24 10:46:43 +00:00 |
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ameyner2
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da8cf2f207
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Added pipeline-specific config files for rnaseq and sarek
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2021-03-24 10:46:26 +00:00 |
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