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FIX: Strict syntax for incliva #1075

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FIX: Strict syntax for incliva #1075

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7abd4d7
conf/incliva.config
maxulysse Apr 7, 2026
f9cee0c
code polish
maxulysse Apr 7, 2026
2901748
Merge branch 'master' into incliva
maxulysse Apr 14, 2026
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57 changes: 12 additions & 45 deletions conf/incliva.config
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Original file line number Diff line number Diff line change
Expand Up @@ -3,55 +3,18 @@ params {
config_profile_description = 'INCLIVA Health Research Institute profile for nf-core.'
config_profile_contact = 'Sheila Zúñiga Trejos - bioinfo@incliva.es'
config_profile_url = 'https://www.incliva.es/en/services/platforms/bioinformatics-unit/'
}

// Function to get hostname
def getHostname() {
def process = 'hostname'.execute()
process.waitFor()
return process.text.trim()
}

// Function to set singularity path according to which host nextflow is running on

def hostname = { getHostname() }

if (hostname == 'vlinuxcervantes3srv') {
System.out.println("\nINFO: working on ${hostname}\n")

// Resources details
params.max_memory = 60.GB
params.max_cpus = 15
singularity.cacheDir = "/nfs/home/software/singularity/nf_cacheDir"

process {
resourceLimits = [
memory: 60.GB,
cpus: 15,
]
}

} else if (hostname == 'vlinuxcervantes4srv') {
System.out.println("\nINFO: working on ${hostname}.\n")

// Resources details
params.max_memory = 120.GB
params.max_cpus = 19
singularity.cacheDir = "/nfs/home/software/singularity/nf_cacheDir"

process {
resourceLimits = [
memory: 120.GB,
cpus: 19,
]
}

} else {
System.err.println("\nERROR: unknown machine. Update incliva.config on nf-core/configs if you are working on another host.\n")
system_hostname = 'hostname'.execute().text.trim() ?: 'unknown'
max_memory = params.system_hostname == 'vlinuxcervantes3srv' ? 60.GB
: params.system_hostname == 'vlinuxcervantes4srv' ? 120.GB
: System.err.println("\nERROR: unknown machine. Update incliva.config on nf-core/configs if you are working on another host.\n")
max_cpus = params.system_hostname == 'vlinuxcervantes3srv' ? 15
: params.system_hostname == 'vlinuxcervantes4srv' ? 19
: System.err.println("\nERROR: unknown machine. Update incliva.config on nf-core/configs if you are working on another host.\n")
}

// Singularity details
singularity {
cacheDir = "/nfs/home/software/singularity/nf_cacheDir"
enabled = true
autoMounts = true
}
Expand All @@ -60,4 +23,8 @@ singularity {
process {
executor = 'local'
maxRetries = 2
resourceLimits = params.max_memory && params.max_cpus ? [
memory: params.max_memory,
cpus: params.max_cpus
] : System.err.println("\nERROR: unknown machine. Update incliva.config on nf-core/configs if you are working on another host.\n")
}
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