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19 changes: 5 additions & 14 deletions conf/wustl_htcf.config
Original file line number Diff line number Diff line change
@@ -1,29 +1,20 @@
// Forked from https://github.com/nf-core/configs/blob/master/conf/prince.config

def labEnvVar = System.getenv("LAB")

if (labEnvVar) {
System.out.println("Lab: " + labEnvVar)
singularityDir = "/ref/$LAB/data/singularity_images_nextflow" // If $LAB is set, use that
} else {
def id = "id -nG".execute().text
def labAutodetect = id.split(" ").last()
System.out.println("Lab: " + labAutodetect)
singularityDir = "/ref/" + labAutodetect + "/data/singularity_images_nextflow"
}

params {
config_profile_description = """
WUSTL High Throughput Computing Facility cluster profile provided by nf-core/configs.
Run from your scratch directory, the output files may be large!
Please consider running the pipeline on a compute node the first time, as it will be pulling the docker image, which will be converted into a singularity image, which is heavy on the login node. Subsequent runs can be done on the login node, as the docker image will only be pulled and converted once. By default, the images will be stored in $singularityDir
Please consider running the pipeline on a compute node the first time, as it will be pulling the docker image, which will be converted into a singularity image, which is heavy on the login node. Subsequent runs can be done on the login node, as the docker image will only be pulled and converted once. By default, the images will be stored in ${params.singularityDir}
""".stripIndent()
config_profile_contact = "Gavin John <gavinjohn@wustl.edu>"
config_profile_url = "https://github.com/nf-core/configs/blob/master/docs/wustl_htcf.md"

max_cpus = 24
max_memory = 750.GB
max_time = 168.h

// Define singularity directory based on LAB environment variable or group membership
singularityDir = "/ref/${System.getenv("LAB") ?: "id -nG".execute().text.split(" ").last()}/data/singularity_images_nextflow"
}

spack {
Expand All @@ -32,7 +23,7 @@ spack {

singularity {
enabled = true
cacheDir = singularityDir
cacheDir = params.singularityDir
}

process {
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