millironx/nf-configs
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Merge pull request #2 from nf-core/master

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Merge commits from nf-core/configs master
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ameynert 2021-03-30 16:09:32 +01:00 committed by GitHub
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3 changed files with 23 additions and 5 deletions
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16
conf/awsbatch.config
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@ -7,10 +7,22 @@ params {
awsqueue = false awsqueue = false
awsregion = 'eu-west-1' awsregion = 'eu-west-1'
awscli = '/home/ec2-user/miniconda/bin/aws' awscli = '/home/ec2-user/miniconda/bin/aws'
tracedir = './' }
timeline {
overwrite = true
}
report {
overwrite = true
}
trace {
overwrite = true
}
dag {
overwrite = true
} }
process.executor = 'awsbatch' process.executor = 'awsbatch'
process.queue = params.awsqueue process.queue = params.awsqueue
aws.region = params.awsregion aws.region = params.awsregion
executor.awscli = params.awscli aws.batch.cliPath = params.awscli

8
conf/jax.config
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@ -2,6 +2,7 @@ params {
config_profile_description = 'The Jackson Laboratory Sumner HPC profile provided by nf-core/configs.' config_profile_description = 'The Jackson Laboratory Sumner HPC profile provided by nf-core/configs.'
config_profile_contact = 'Asaf Peer (@peera)' config_profile_contact = 'Asaf Peer (@peera)'
config_profile_url = 'https://jacksonlaboratory.sharepoint.com/sites/ResearchIT/SitePages/Welcome-to-Sumner.aspx' config_profile_url = 'https://jacksonlaboratory.sharepoint.com/sites/ResearchIT/SitePages/Welcome-to-Sumner.aspx'
singularity_cache_dir = '/fastscratch/singularity_cache_nfcore'
} }
executor.$slurm.queueSize = 250 executor.$slurm.queueSize = 250
@ -12,8 +13,11 @@ process {
module = "slurm" module = "slurm"
beforeScript = 'module load singularity' beforeScript = 'module load singularity'
} }
singularity.enabled = true singularity{
singularity.autoMounts = true enabled = true
autoMounts = true
cacheDir = params.singularity_cache_dir
}
params { params {
max_memory = 768.GB max_memory = 768.GB
max_cpus = 70 max_cpus = 70

4
docs/awsbatch.md
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@ -1,4 +1,6 @@
# nf-core/configs: awsbatch Configuration # nf-core/configs: awsbatch Configuration
To be used with `awsbatch`. To be used with `awsbatch`.
Custom queue, region and CLI path can be supplied with `params.awsqueue`, `params.awsregion`, `params.awscli`, respectively. Custom queue and region can be supplied with `params.awsqueue`, `params.awsregion`, `params.awscli`, respectively.
Allow `overwrite` of `trace`, `timeline`, `report` and `dag` to allow resuming pipelines.