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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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116
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 {
aahz {
params { params {
{{ if (eq .chezmoi.hostname "ceres") }} config_profile_description = 'KSU VDL Molecular NGS Big Server profile'
max_memory = 768.GB config_profile_contact = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>'
max_cpus = 40 config_profile_url = null
max_time = 1000.h
{{ end }} max_memory = 745.GB
{{ if (or (eq .chezmoi.hostname "Atlas-login-1") (eq .chezmoi.hostname "Atlas-login-2")) }} max_cpus = 78
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_memory = 1539.GB
max_cpus = 24 max_cpus = 24
max_time = 14.d max_time = 14.d
{{ end }}
} }
singularity {
enabled = true
autoMounts = true
envWhitelist = 'NCBI_API_KEY'
}
process { process {
scratch = true scratch = true
executor = 'slurm' executor = 'slurm'
clusterOptions = '--account=fabadru' clusterOptions = '--account=fabadru'
{{ if (or (eq .chezmoi.hostname "Atlas-login-1") (eq .chezmoi.hostname "Atlas-login-2")) }}
cpus = 12
memory = 192.GB
time = 7.d
withLabel: process_high_memory { withLabel: process_high_memory {
queue = 'bigmem' queue = 'bigmem'
memory = 1536.GB
} }
withLabel: process_long {
time = 14.d
} }
withLabel: process_medium {
cpus = 12
memory = 192.GB
time = 7.d
} }
withLabel: process_high { ceres {
cpus = 24 params {
memory = 384.GB config_profile_description = 'USDA ARS SCInet Ceres Cluster profile'
time = 14.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
} }
{{ end }} singularity {
{{ if (eq .chezmoi.hostname "ceres") }} enabled = true
autoMounts = true
envWhitelist = 'NCBI_API_KEY'
}
process {
scratch = true
executor = 'slurm'
queue = 'short' queue = 'short'
cpus = 18
memory = 54.GB
time = 24.h
withLabel: process_high_memory { withLabel: process_high_memory {
queue = 'mem' queue = 'mem'
memory = 640.GB
} }
withLabel: process_long { withLabel: process_long {
queue = 'long' queue = 'long'
time = 21.d
} }
withLabel: process_medium { withLabel: process_medium {
queue = '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 }} }
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'
}
}
}