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Merge pull request #294 from ewels/master

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UPPMAX profile - minor tweaks
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Phil Ewels 2021-11-03 00:02:17 +01:00 committed by GitHub
commit 556a1cf344
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1 changed files with 28 additions and 18 deletions
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46
conf/uppmax.config
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@ -1,11 +1,19 @@
// Profile config names for nf-core/configs
// UPPMAX Config Profile
params {
config_profile_description = 'Swedish UPPMAX cluster profile provided by nf-core/configs.'
// Description is overwritten for other clusters below
config_profile_description = 'UPPMAX (Bianca) cluster profile provided by nf-core/configs.'
config_profile_contact = 'Phil Ewels (@ewels)'
config_profile_url = 'https://www.uppmax.uu.se/'
project = null
clusterOptions = null
schema_ignore_params = "genomes,input_paths,cluster-options,clusterOptions,project"
save_reference = true
// Defaults set for Bianca - other clusters set below
max_memory = 500.GB
max_cpus = 16
max_time = 240.h
// illumina iGenomes reference file paths on UPPMAX
igenomes_base = '/sw/data/igenomes/'
}
singularity {
@ -15,7 +23,7 @@ singularity {
def hostname = "r1"
try {
hostname = "sinfo --local -N -h | grep -F -v CLUSTER: | head -1 | cut -f1 -d' ' ".execute().text.trim()
hostname = "sinfo --local -N -h | grep -m 1 -F -v CLUSTER: | cut -f1 -d' ' ".execute().text.trim()
} catch (java.io.IOException e) {
System.err.println("WARNING: Could not run sinfo to determine current cluster, defaulting to rackham")
}
@ -24,7 +32,7 @@ try {
def clusterOptionsCreator = { m ->
String base = "-A $params.project ${params.clusterOptions ?: ''}"
// Do not use -p node on irma or if a thin node/core is enough
if (m <= 125.GB || hostname ==~ "i.*") {
if (m <= 125.GB || hostname.startsWith("i")) {
return base
}
@ -34,7 +42,7 @@ def clusterOptionsCreator = { m ->
// Use mem1TB for remaining cases on rackham (no 512 Gbyte nodes)
if (hostname ==~ "r.*") {
if (hostname.startsWith("r")) {
return base + " -p node -C mem1TB "
}
@ -54,30 +62,32 @@ process {
scratch = '$SNIC_TMP'
}
params {
save_reference = true
max_memory = 500.GB
max_cpus = 16
max_time = 240.h
// illumina iGenomes reference file paths on UPPMAX
igenomes_base = '/sw/data/igenomes/'
}
if (hostname ==~ "s[0-9][0-9]*") {
// Cluster: Snowy
// Caution: Bianca nodes will be project name-nodenumber, e.g. sens2021500-001
// so cannot rely on just starting with 's'
if (hostname.matches("^s[0-9][0-9]*")) {
params.max_time = 700.h
params.max_memory = 3880.GB
params.config_profile_description = 'UPPMAX (Snowy) cluster profile provided by nf-core/configs.'
}
if (hostname ==~ "i.*") {
// Cluster: Irma
if (hostname.startsWith("i")) {
params.max_memory = 250.GB
params.config_profile_description = 'UPPMAX (Irma) cluster profile provided by nf-core/configs.'
}
if (hostname ==~ "r.*") {
// Cluster: Rackham
if (hostname.startsWith("r")) {
params.max_cpus = 20
params.max_memory = 970.GB
params.config_profile_description = 'UPPMAX (Rackham) cluster profile provided by nf-core/configs.'
}
// Cluster: Bianca - set in initial params block above
// Additional devel profile for running in devel queue
// Run with `-profile upppmax,devel`
profiles {
devel {
params {