Remove empty resourceLimit entries

nf-core · Sep 23, 2024 · c5822f8 · c5822f8
1 parent 32a6072
commit c5822f8
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Showing 21 changed files with 12 additions and 101 deletions.
diff --git a/conf/bigpurple.config b/conf/bigpurple.config
@@ -18,11 +18,6 @@ singularity {
 }
 
 process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
     beforeScript = """
     module load singularity/3.1
     module load squashfs-tools/4.3

diff --git a/conf/csiro_petrichor.config b/conf/csiro_petrichor.config
@@ -19,11 +19,6 @@ singularity {
 
 // Define process resource limits
 process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
     executor       = 'slurm'
     clusterOptions = "--account=${System.getenv('SBATCH_ACCOUNT')}"
     module         = 'singularity/3.8.7'

diff --git a/conf/ebi_codon.config b/conf/ebi_codon.config
@@ -20,11 +20,6 @@ singularity {
 }
 
 process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
     queue         = {
         if (task.time > 7.day && task.memory > 300.GB) {
             "long_bigmem"

diff --git a/conf/ebi_codon_slurm.config b/conf/ebi_codon_slurm.config
@@ -20,11 +20,6 @@ singularity {
 }
 
 process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
     // this is to avoid errors for missing files due to shared filesystem latency
     maxRetries    = 3
     errorStrategy = { task.exitStatus == 0 ? "retry" : "terminate" }

diff --git a/conf/embl_hd.config b/conf/embl_hd.config
@@ -14,11 +14,6 @@ apptainer {
 }
 
 process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
     def scratch_dir = System.getenv("SCRATCHDIR")
     maxRetries = 3
     cache = 'lenient'

diff --git a/conf/gis.config b/conf/gis.config
@@ -6,11 +6,6 @@ params {
 }
 
 process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
     executor       = 'sge'
     clusterOptions = { "-l mem_free=" + task.memory.toString().replaceAll(/[\sB]/, '') }
     penv           = 'OpenMP'

diff --git a/conf/googlebatch.config b/conf/googlebatch.config
@@ -25,11 +25,6 @@ params {
 workDir = params.workdir_bucket
 
 process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
     executor = 'google-batch'
 }
 google {

diff --git a/conf/googlels.config b/conf/googlels.config
@@ -24,11 +24,6 @@ params {
 workDir = params.workdir_bucket
 
 process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
     executor = 'google-lifesciences'
 }
 google {

diff --git a/conf/mccleary.config b/conf/mccleary.config
@@ -24,12 +24,11 @@ executor {
 process {
     resourceLimits = [
         memory: 983.GB,
-        cpus: 64,
-        time: 
+        cpus: 64
     ]
-    queue    = { task.time > 24.h ? 'week' : 'day' }
-    scratch  = 'true'
-    executor = 'slurm'
+    queue          = { task.time > 24.h ? 'week' : 'day' }
+    scratch        = 'true'
+    executor       = 'slurm'
 }
 
 params {

diff --git a/conf/nci_gadi.config b/conf/nci_gadi.config
@@ -24,11 +24,6 @@ executor {
 
 // Define process resource limits
 process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
     executor = 'pbspro'
     project = System.getenv("PROJECT")
     storage = 'scratch/params.project'

diff --git a/conf/nygc.config b/conf/nygc.config
@@ -8,11 +8,6 @@ singularity {
 }
 
 process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
     executor = 'slurm'
     queue    = { task.accelerator ? 'gpu' : (task.memory > 100.GB ? 'bigmem' : 'pe2') }
 }

diff --git a/conf/pawsey_setonix.config b/conf/pawsey_setonix.config
@@ -24,8 +24,7 @@ executor {
 process {
     resourceLimits = [
         memory: 230.Gb,
-        cpus: 64,
-        time: 
+        cpus: 64
     ]
     executor       = 'slurm'
     clusterOptions = "--account=${System.getenv('PAWSEY_PROJECT')}"

diff --git a/conf/qmul_apocrita.config b/conf/qmul_apocrita.config
@@ -12,11 +12,6 @@ executor {
 apptainer.runOptions = "-B ${HOME},${PWD}"
 
 process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
 
     //NEED TO SET PARALLEL ENVIRONMENT TO SMP SO MULTIPLE CPUS CAN BE SUBMITTED
     penv           = 'smp'

diff --git a/conf/roslin.config b/conf/roslin.config
@@ -10,11 +10,6 @@ executor {
 }
 
 process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
     stageInMode = 'symlink'
     scratch = 'false'
     penv = { task.cpus > 1 ? "sharedmem" : null }

diff --git a/conf/software_license.config b/conf/software_license.config
@@ -10,11 +10,6 @@ params {
 
 if (params.sentieon_extension) {
     process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
         withLabel: 'sentieon' {
             ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64 ?: ''
             ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64 ?: ''

diff --git a/conf/tubingen_apg.config b/conf/tubingen_apg.config
@@ -13,12 +13,11 @@ cleanup = true
 process {
     resourceLimits = [
         memory: 4.TB,
-        cpus: 256,
-        time: 
+        cpus: 256
     ]
-    executor   = 'slurm'
-    queue      = { task.time <= 2.h ? 'short' : task.time <= 48.h ? 'medium' : 'long' }
-    maxRetries = 2
+    executor       = 'slurm'
+    queue          = { task.time <= 2.h ? 'short' : task.time <= 48.h ? 'medium' : 'long' }
+    maxRetries     = 2
 }
 
 executor {

diff --git a/conf/ucd_sonic.config b/conf/ucd_sonic.config
@@ -8,11 +8,6 @@ params {
 }
 
 process {
-resourceLimits = [
-    memory: ,
-    cpus: 40,
-    time: 12.h
-]
     executor        = 'slurm'
     queue           = 'shared'
     queueSize       = 50

diff --git a/conf/ucl_cscluster.config b/conf/ucl_cscluster.config
@@ -12,11 +12,6 @@ executor {
 singularity.runOptions = "-B ${HOME},${PWD}"
 
 process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
 
     //NEED TO SET PARALLEL ENVIRONMENT TO SMP SO MULTIPLE CPUS CAN BE SUBMITTED
     penv           = 'smp'

diff --git a/conf/ucl_myriad.config b/conf/ucl_myriad.config
@@ -12,11 +12,6 @@ executor {
 apptainer.runOptions = "-B ${HOME},${PWD}"
 
 process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
 
     //NEED TO SET PARALLEL ENVIRONMENT TO SMP SO MULTIPLE CPUS CAN BE SUBMITTED
     penv           = 'smp'

diff --git a/conf/unc_lccc.config b/conf/unc_lccc.config
@@ -7,11 +7,10 @@ params {
 process {
     resourceLimits = [
         memory: 950.GB,
-        cpus: 90,
-        time: 
+        cpus: 90
     ]
-    executor = "slurm"
-    queue    = "allnodes"
+    executor       = "slurm"
+    queue          = "allnodes"
 }
 
 singularity {

diff --git a/conf/york_viking.config b/conf/york_viking.config
@@ -21,11 +21,6 @@ apptainer {
 }
 
 process {
-resourceLimits = [
-    memory: ,
-    cpus: ,
-    time: 
-]
     maxRetries     = 3
     clusterOptions = "--get-user-env --account=${System.getenv('USER_ACCOUNT')}"
     // Get user environment and assign account