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Add mamba to Nextflow config

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This commit is contained in:
Thomas A. Christensen II 2022-07-21 11:05:57 -05:00
parent 0c81dcaff9
commit e349d9968f
Signed by: millironx
GPG key ID: 139C07724802BC5D
1 changed files with 2 additions and 94 deletions
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96
dot_nextflow/config.tmpl
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@ -4,99 +4,7 @@ tower {
accessToken = '{{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }}' accessToken = '{{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }}'
} }
{{ end }} {{ end }}
profiles {
aahz {
params {
config_profile_description = 'KSU VDL Molecular NGS Big Server profile'
config_profile_contact = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>'
config_profile_url = null
max_memory = 745.GB conda {
max_cpus = 78 useMamba = true
max_time = 7.d
}
singularity {
enabled = true
autoMounts = true
envWhitelist = 'NCBI_API_KEY'
}
process {
executor = 'local'
}
}
atlas {
params {
config_profile_description = 'Mississippi State University Atlas Cluster profile'
config_profile_contact = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>'
config_profile_url = 'https://www.hpc.msstate.edu/computing/atlas/'
max_memory = 1539.GB
max_cpus = 24
max_time = 14.d
}
singularity {
enabled = true
autoMounts = true
envWhitelist = 'NCBI_API_KEY'
}
process {
scratch = true
executor = 'slurm'
clusterOptions = '--account=fabadru'
withLabel: process_high_memory {
queue = 'bigmem'
}
}
}
ceres {
params {
config_profile_description = 'USDA ARS SCInet Ceres Cluster profile'
config_profile_contact = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>'
config_profile_url = 'https://scinet.usda.gov/guide/ceres/#partitions-or-queues'
max_memory = 768.GB
max_cpus = 40
max_time = 1000.h
}
singularity {
enabled = true
autoMounts = true
envWhitelist = 'NCBI_API_KEY'
}
process {
scratch = true
executor = 'slurm'
queue = 'short'
withLabel: process_high_memory {
queue = 'mem'
}
withLabel: process_long {
queue = 'long'
}
withLabel: process_medium {
queue = 'medium'
}
}
}
tananda {
params {
config_profile_description = 'KSU VDL Molecular NGS Desktop profile'
config_profile_contact = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>'
config_profile_url = null
max_memory = 14.GB
max_cpus = 12
max_time = 4.h
}
docker {
enabled = true
userEmulation = true
envWhitelist = 'NCBI_API_KEY'
}
process {
executor = 'local'
}
}
} }