updating resources labels

caravagnalab · Jan 27, 2025 · 98f8875 · 98f8875
1 parent 9129bea
commit 98f8875
Show file tree

Hide file tree

Showing 14 changed files with 4 additions and 47 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -40,7 +40,9 @@ process {
         memory = { 100.GB * task.attempt }
         time   = { 5.h   * task.attempt }
     }
-    withLabel:process_long {
+    withLabel:process_low_long {
+        cpus   = { 8     * task.attempt }
+        memory = { 12.GB * task.attempt }
         time   = { 5.h  * task.attempt }
     }
     withLabel:error_ignore {

diff --git a/conf/modules/cnaqc.config b/conf/modules/cnaqc.config
@@ -1,9 +1,5 @@
 process {
     withName: 'CNAQC'{
-        memory = '20 GB'
-        cpus = 4
-        time = '30 min'
-
         errorStrategy = 'retry'
         publishDir = [
             [
@@ -37,10 +33,6 @@ process {
 
 
     withName: 'JOIN_CNAQC'{
-        memory = '20 GB'
-        cpus = 4
-        time = '30 min'
-
         errorStrategy = 'retry'
 
         publishDir = [

diff --git a/conf/modules/ctree.config b/conf/modules/ctree.config
@@ -1,7 +1,5 @@
 process {
     withName: 'CTREE' {
-        memory='50 GB'
-        time='2h'
         errorStrategy='ignore'
         publishDir = [
             [

diff --git a/conf/modules/driver_annotation.config b/conf/modules/driver_annotation.config
@@ -1,7 +1,5 @@
 process{
     withName: 'ANNOTATE_DRIVER' {
-        memory = '15 GB'
-        time = '15 min'
         errorStrategy = 'finish'
         publishDir = [
                 [

diff --git a/conf/modules/ensemblvep.config b/conf/modules/ensemblvep.config
@@ -27,8 +27,6 @@ process {
 
 process {
     withName: 'TABIX_TABIX'{
-        memory = '2 GB'
-        time = '1h'
         publishDir = [
             [
                 mode: params.publish_dir_mode,
@@ -41,8 +39,6 @@ process {
 
 process {
     withName: 'UNTAR'{
-        memory = '2 GB'
-        time = '1h'
         publishDir = [
             [
                 mode: params.publish_dir_mode,

diff --git a/conf/modules/formatter.config b/conf/modules/formatter.config
@@ -1,8 +1,5 @@
 process {
     withName: 'CNA_PROCESSING'{
-        memory = '10 GB'
-        cpus = 4
-        time = '30 min'
         errorStrategy = 'retry'
         publishDir = [
             [
@@ -14,9 +11,6 @@ process {
     }
 
     withName: 'VCF_PROCESSING'{
-        memory = '10 GB'
-        cpus = 4
-        time = '30 min'
         errorStrategy = 'retry'
         ext.args = {[
             "filter_mutations": params.vcf_filter_mutations
@@ -30,9 +24,6 @@ process {
         ]
     }
     withName: 'RDS_PROCESSING'{
-        memory = '10 GB'
-        cpus = 4
-        time = '30 min'
         errorStrategy = 'retry'
         publishDir = [
             [

diff --git a/conf/modules/lifter.config b/conf/modules/lifter.config
@@ -7,8 +7,6 @@ process{
                     pattern: "*{rds}"
                 ]
         ]
-        memory = '10 GB'
-        time = '10 min'
         errorStrategy = 'finish'
     }
 
@@ -19,8 +17,6 @@ process{
                     path: { "${params.outdir}/lifter/positions/${meta.dataset}/${meta.patient}/"}
                 ]
         ]
-        memory = '10 GB'
-        time = '10 min'
         errorStrategy = 'finish'
     }
 
@@ -32,8 +28,6 @@ process{
                 pattern: "*{rds}"
             ]
         ]
-        memory = '10 GB'
-        time = '10 min'
         errorStrategy = 'finish'
     }
 

diff --git a/conf/modules/mobsterh.config b/conf/modules/mobsterh.config
@@ -1,7 +1,5 @@
 process {
     withName: 'MOBSTERh' {
-        memory='128 GB'
-        time='2h'
         publishDir = [
             [
                 mode: params.publish_dir_mode,

diff --git a/conf/modules/pyclonevi.config b/conf/modules/pyclonevi.config
@@ -1,7 +1,5 @@
 process {
     withName: 'PYCLONEVI' {
-        memory='50 GB'
-        time='2h'
         publishDir = [
             [
                 mode: params.publish_dir_mode,

diff --git a/conf/modules/sigprofiler.config b/conf/modules/sigprofiler.config
@@ -15,10 +15,7 @@ process {
 
 process {
     withName: 'SIGPROFILER' {
-        memory = "100 GB"
-        time = "12.h"
         singularity.runOptions = '--writable-tmpfs'
-        cpus = 12
         maxForks = 20
         errorStrategy = 'retry'
         ext.args = {

diff --git a/conf/modules/sparsesignatures.config b/conf/modules/sparsesignatures.config
@@ -1,7 +1,5 @@
 process {
     withName: 'SPARSE_SIGNATURES'{
-        memory = '150 GB'
-        time = '12h'
         errorStrategy = 'finish'
         ext.args = {[
             "K" : params.sparsesignatures_K,

diff --git a/conf/modules/tinc.config b/conf/modules/tinc.config
@@ -1,8 +1,5 @@
 process {
     withName: 'TINC'{
-        memory='16 GB'
-        cpus='4'
-        time='6h'
         errorStrategy='finish'
         ext.args = {[
             "vaf_range_tumour" : params.tinc_vaf_range_tumour,

diff --git a/conf/modules/viber.config b/conf/modules/viber.config
@@ -1,7 +1,5 @@
 process {
     withName: 'VIBER' {
-        memory='128 GB'
-        time='2h'
         errorStrategy = 'ignore'
         publishDir = [
             [

diff --git a/modules/local/SparseSignatures/main.nf b/modules/local/SparseSignatures/main.nf
@@ -1,6 +1,6 @@
 process SPARSE_SIGNATURES {
     tag "$meta.id"
-    label "process_long"
+    label "process_low_long"
     container = 'docker://lvaleriani/sparsesignature:version1.0'
 
     input: