Add resources selectors

caravagnalab · Jan 23, 2025 · 08c3df0 · 08c3df0
1 parent 50eb4c9
commit 08c3df0
Show file tree

Hide file tree

Showing 22 changed files with 42 additions and 42 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -9,11 +9,10 @@
 */
 
 process {
-
     // TODO nf-core: Check the defaults for all processes
     cpus   = { 1      * task.attempt }
     memory = { 6.GB   * task.attempt }
-    time   = { 4.h    * task.attempt }
+    time   = { 2.h    * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
@@ -29,28 +28,20 @@ process {
     withLabel:process_single {
         cpus   = { 1                   }
         memory = { 6.GB * task.attempt }
-        time   = { 4.h  * task.attempt }
+        time   = { 2.h  * task.attempt }
     }
     withLabel:process_low {
-        cpus   = { 2     * task.attempt }
+        cpus   = { 8     * task.attempt }
         memory = { 12.GB * task.attempt }
-        time   = { 4.h   * task.attempt }
-    }
-    withLabel:process_medium {
-        cpus   = { 6     * task.attempt }
-        memory = { 36.GB * task.attempt }
-        time   = { 8.h   * task.attempt }
+        time   = { 2.h   * task.attempt }
     }
     withLabel:process_high {
-        cpus   = { 12    * task.attempt }
-        memory = { 72.GB * task.attempt }
-        time   = { 16.h  * task.attempt }
+        cpus   = { 20     * task.attempt }
+        memory = { 100.GB * task.attempt }
+        time   = { 5.h   * task.attempt }
     }
     withLabel:process_long {
-        time   = { 20.h  * task.attempt }
-    }
-    withLabel:process_high_memory {
-        memory = { 200.GB * task.attempt }
+        time   = { 5.h  * task.attempt }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'

diff --git a/modules/local/CNAqc/main.nf b/modules/local/CNAqc/main.nf
@@ -1,5 +1,6 @@
 process CNAQC {
     tag "$meta.id"
+    label "process_low"
     container = 'docker://lvaleriani/cnaqc:version1.0'
 
     input:

diff --git a/modules/local/CNAqc2tsv/main.nf b/modules/local/CNAqc2tsv/main.nf
@@ -4,6 +4,7 @@
 
 process RDS_PROCESSING {
     tag "$meta.id"
+    label "process_single"
     container = 'docker://lvaleriani/cnaqc:version1.0'
 
     input:

diff --git a/modules/local/SigProfiler/SigProfiler/main.nf b/modules/local/SigProfiler/SigProfiler/main.nf
@@ -1,5 +1,6 @@
 process SIGPROFILER {
     tag "$meta.id"
+    label "process_high"
     container = 'docker://katiad/sigprofiler:version1.0'
 
     input:
@@ -161,8 +162,8 @@ process SIGPROFILER {
 
         with open('versions.yml', 'a') as f:
             f.write('"${task.process}":'+"\\n")
-            f.write("\tSigProfilerMatrixGenerator: "+SigProfilerMatrixGenerator_version+"\\n")
-            f.write("\tSigProfilerExtractor: "+SigProfilerExtractor_version+"\\n")
+            f.write("    SigProfilerMatrixGenerator: "+SigProfilerMatrixGenerator_version+"\\n")
+            f.write("    SigProfilerExtractor: "+SigProfilerExtractor_version+"\\n")
 
     """
 

diff --git a/modules/local/SigProfiler/download/main.nf b/modules/local/SigProfiler/download/main.nf
@@ -1,4 +1,5 @@
 process DOWNLOAD_GENOME_SIGPROFILER {
+    label "process_single"
     container = 'docker://katiad/sigprofiler:version1.0'
 
     input:

diff --git a/modules/local/SparseSignatures/main.nf b/modules/local/SparseSignatures/main.nf
@@ -1,8 +1,8 @@
 process SPARSE_SIGNATURES {
     tag "$meta.id"
+    label "process_long"
     container = 'docker://lvaleriani/sparsesignature:version1.0'
 
-
     input:
 
         tuple val(meta), path(tsv_join,  stageAs: '*.tsv')
@@ -16,7 +16,6 @@ process SPARSE_SIGNATURES {
         path "versions.yml", emit: versions
 
     script:
-
     def args                         = task.ext.args
     def prefix                       = task.ext.prefix                                    ?: "${meta.id}"
     def K                            = args!='' && args.K                                 ? "$args.K" : ""

diff --git a/modules/local/annotate_driver/main.nf b/modules/local/annotate_driver/main.nf
@@ -1,6 +1,7 @@
 
 process ANNOTATE_DRIVER {
     tag "$meta.id"
+    label "process_single"
     container = 'docker://lvaleriani/cnaqc:version1.0'
 
     input:

diff --git a/modules/local/cna2CNAqc/main.nf b/modules/local/cna2CNAqc/main.nf
@@ -1,6 +1,6 @@
 process CNA_PROCESSING {
     tag "$meta.id"
-
+    label "process_single"
     container "docker://lvaleriani/cnaqc:version1.0"
 
     input:

diff --git a/modules/local/ctree/main.nf b/modules/local/ctree/main.nf
@@ -1,9 +1,9 @@
 process CTREE {
     tag "$meta.id"
+    label "process_low"
     container = 'docker://elenabuscaroli/ctree:version1.1'
 
     input:
-
         tuple val(meta), path(ctree_input)
 
     output:
@@ -15,7 +15,6 @@ process CTREE {
         path "versions.yml", emit: versions
 
     script:
-
     def args = task.ext.args ?: ""
     def prefix = task.ext.prefix ?: "${meta.id}"
     def sspace_cutoff = args!="" && args.sspace_cutoff ? "$args.sspace_cutoff" : ""

diff --git a/modules/local/get_positions/main.nf b/modules/local/get_positions/main.nf
@@ -1,5 +1,6 @@
 process GET_POSITIONS_ALL {
     tag "$meta.id"
+    label "process_single"
     container = 'docker://lvaleriani/cnaqc:version1.0'
 
     input:

diff --git a/modules/local/get_positions/main_rel.nf b/modules/local/get_positions/main_rel.nf
@@ -1,5 +1,6 @@
 process GET_POSITIONS_REL {
     tag "$meta.id"
+    label "process_single"
     container = 'docker://lvaleriani/cnaqc:dev1'
 
     input:

diff --git a/modules/local/join_CNAqc/main.nf b/modules/local/join_CNAqc/main.nf
@@ -1,5 +1,6 @@
 process JOIN_CNAQC {
     tag "$meta.id"
+    label "process_low"
     container = 'docker://lvaleriani/cnaqc:version1.0'
 
     input:

diff --git a/modules/local/join_positions/main.nf b/modules/local/join_positions/main.nf
@@ -1,5 +1,6 @@
 process JOIN_POSITIONS {
     tag "$meta.id"
+    label "process_single"
     container = 'docker://lvaleriani/cnaqc:version1.0'
 
     input:

diff --git a/modules/local/mobsterh/main.nf b/modules/local/mobsterh/main.nf
@@ -1,5 +1,6 @@
 process MOBSTERh {
     tag "$meta.id"
+    label "process_single"
     container = 'docker://elenabuscaroli/mobster:version1.0'
 
     input:

diff --git a/modules/local/pyclonevi/main.nf b/modules/local/pyclonevi/main.nf
@@ -1,5 +1,6 @@
 process PYCLONEVI {
     tag "$meta.id"
+    label "process_low"
     container = 'https://depot.galaxyproject.org/singularity/pyclone-vi%3A0.1.3--pyhca03a8a_0'
 
     input:

diff --git a/modules/local/tinc/main.nf b/modules/local/tinc/main.nf
@@ -1,8 +1,9 @@
 process TINC {
-
     tag "$meta.id"
+    label "process_single"
     container 'docker://vvvirgy/tinc:v2' // define the running container
     // conda "${moduleDir}/environment.yml"
+
     input:
         tuple val(meta), path(cna_RDS), path(snv_RDS)
 
@@ -14,7 +15,6 @@ process TINC {
         path "versions.yml", emit: versions
 
     script:
-
     def args                                = task.ext.args
     def prefix                              = task.ext.prefix                                       ?: "${meta.id}"
     def vaf_range_tumour                    = args!='' && args.vaf_range_tumour                     ?  "$args.vaf_range_tumour"  : ""

diff --git a/modules/local/vcf2CNAqc/main.nf b/modules/local/vcf2CNAqc/main.nf
@@ -1,6 +1,6 @@
 process VCF_PROCESSING {
     tag "$meta.id"
-
+    label "process_single"
     container "docker://lvaleriani/cnaqc:version1.0"
 
     input:

diff --git a/modules/local/viber/main.nf b/modules/local/viber/main.nf
@@ -1,21 +1,22 @@
 process VIBER {
     tag "$meta.id"
+    label "process_single"
     container = 'docker://elenabuscaroli/viber:version0.1'
 
     input:
-    tuple val(meta), path(rds_join), val(tumour_samples) //rds from either JOIN_CNAQC or JOIN_FIT, should be always grouped
+        tuple val(meta), path(rds_join), val(tumour_samples) //rds from either JOIN_CNAQC or JOIN_FIT, should be always grouped
 
     output:
-    tuple val(meta), path("*_viber_best_st_fit.rds"), emit: viber_rds
-    tuple val(meta), path("*_viber_best_st_heuristic_fit.rds"), emit: viber_heuristic_rds
-    tuple val(meta), path("*_${plot1}"), emit: viber_plots_rds
-    tuple val(meta), path("*_${plot2}"), emit: viber_heuristic_plots_rds
-    tuple val(meta), path("*_REPORT_plots_viber.rds"), emit: viber_report_rds
-    tuple val(meta), path("*_REPORT_plots_viber.pdf"), emit: viber_report_pdf
-    tuple val(meta), path("*_REPORT_plots_viber.png"), emit: viber_report_png
-    path "versions.yml", emit: versions
-
-script:
+        tuple val(meta), path("*_viber_best_st_fit.rds"), emit: viber_rds
+        tuple val(meta), path("*_viber_best_st_heuristic_fit.rds"), emit: viber_heuristic_rds
+        tuple val(meta), path("*_${plot1}"), emit: viber_plots_rds
+        tuple val(meta), path("*_${plot2}"), emit: viber_heuristic_plots_rds
+        tuple val(meta), path("*_REPORT_plots_viber.rds"), emit: viber_report_rds
+        tuple val(meta), path("*_REPORT_plots_viber.pdf"), emit: viber_report_pdf
+        tuple val(meta), path("*_REPORT_plots_viber.png"), emit: viber_report_png
+        path "versions.yml", emit: versions
+
+    script:
     // viber fit params
     def args = task.ext.args ?: ""
     def prefix = task.ext.prefix ?:"${meta.id}"

diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf
diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf
diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf
diff --git a/modules/nf-core/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf