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Refactor Nextflow config to profiles

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Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
This commit is contained in:
Thomas A. Christensen II 2022-03-08 09:36:52 -06:00
parent 3d373a25b5
commit aae9718f59
Signed by: millironx
GPG key ID: 139C07724802BC5D
1 changed files with 90 additions and 66 deletions
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156
dot_nextflow/config.tmpl
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@ -2,75 +2,99 @@ tower {
enabled = true enabled = true
accessToken = '{{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }}' accessToken = '{{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }}'
} }
{{ if (eq .cluster "scinet") }} profiles {
params { aahz {
{{ if (eq .chezmoi.hostname "ceres") }} params {
max_memory = 768.GB config_profile_description = 'KSU VDL Molecular NGS Big Server profile'
max_cpus = 40 config_profile_contact = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>'
max_time = 1000.h config_profile_url = null
{{ end }}
{{ if (or (eq .chezmoi.hostname "Atlas-login-1") (eq .chezmoi.hostname "Atlas-login-2")) }}
max_memory = 1539.GB
max_cpus = 24
max_time = 14.d
{{ end }}
}
process { max_memory = 745.GB
scratch = true max_cpus = 78
executor = 'slurm' max_time = 7.d
clusterOptions = '--account=fabadru' }
{{ if (or (eq .chezmoi.hostname "Atlas-login-1") (eq .chezmoi.hostname "Atlas-login-2")) }} singularity {
cpus = 12 enabled = true
memory = 192.GB autoMounts = true
time = 7.d envWhitelist = 'NCBI_API_KEY'
withLabel: process_high_memory { }
queue = 'bigmem' process {
memory = 1536.GB executor = 'local'
}
} }
withLabel: process_long { atlas {
time = 14.d 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'
}
}
} }
withLabel: process_medium { ceres {
cpus = 12 params {
memory = 192.GB config_profile_description = 'USDA ARS SCInet Ceres Cluster profile'
time = 7.d 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'
}
}
} }
withLabel: process_high { tananda {
cpus = 24 params {
memory = 384.GB config_profile_description = 'KSU VDL Molecular NGS Desktop profile'
time = 14.d config_profile_contact = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>'
} config_profile_url = null
{{ end }}
{{ if (eq .chezmoi.hostname "ceres") }} max_memory = 14.GB
queue = 'short' max_cpus = 12
cpus = 18 max_time = 4.h
memory = 54.GB }
time = 24.h docker {
withLabel: process_high_memory { enabled = true
queue = 'mem' userEmulation = true
memory = 640.GB envWhitelist = 'NCBI_API_KEY'
} }
withLabel: process_long { process {
queue = 'long' executor = 'local'
time = 21.d }
}
withLabel: process_medium {
queue = 'medium'
cpus = 36
time = 7.d
}
withLabel: process_high {
queue = 'long'
cpus = 36
time = 21.d
}
{{ end }}
withLabel: process_low {
cpus = 2
memory = 4.GB
time = 1.h
{{ if (eq .chezmoi.hostname "ceres") }}queue = 'short'{{ end }}
} }
} }
{{ end }}