Add memory labels and improve default config

Ensembl · Jan 6, 2023 · 09b638a · 09b638a
1 parent 2dcd542
commit 09b638a
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Showing 4 changed files with 18 additions and 22 deletions.
diff --git a/nextflow/ProteinFunction/nextflow.config b/nextflow/ProteinFunction/nextflow.config
@@ -8,29 +8,25 @@ profiles {
   }
 
   lsf {
-    process {
-      executor = 'lsf'
-      queue = 'production'
-      // withLabel: default {
-      //   clusterOptions = '-R"select[mem>2000] rusage[mem=2000]" -M2000'
-      // }
-      // withLabel: medmem {
-      //   clusterOptions = '-R"select[mem>8000] rusage[mem=8000]" -M8000'
-      // }
-      // withLabel: urgent {
-      //  clusterOptions = '-R"select[mem>2000] rusage[mem=2000]" -M2000'
-      // }
-      // withLabel: higmem {
-      //   clusterOptions = '-R"select[mem>16000] rusage[mem=16000]" -M16000'
-      // }
-      // withLabel: long {
-      //   clusterOptions = '-R"select[mem>2000] rusage[mem=2000]" -M2000'
-      // }
+    executor {
+      name = 'lsf'
+      queueSize = 500
+      submitRateLimit = '100/1sec'
     }
+
     singularity {
       enabled = true
       autoMounts = true
     }
+
+    process {
+      queue = 'production'
+      memory = '2GB'
+      withLabel: medmem { memory =  '8 GB' }
+      withLabel: urgent { memory =  '2 GB' }
+      withLabel: higmem { memory = '24 GB' }
+      withLabel: long   { memory =  '2 GB' }
+    }
   }
 
   //untested 

diff --git a/nextflow/ProteinFunction/nf_modules/polyphen2.nf b/nextflow/ProteinFunction/nf_modules/polyphen2.nf
@@ -29,7 +29,7 @@ process run_pph2_on_all_aminoacid_substitutions {
   tag "${peptide.md5}"
   container "ensemblorg/polyphen-2:2.2.3"
   containerOptions "--bind ${params.pph_data}:/opt/pph2/data"
-  memory '4 GB'
+  label 'highmem'
   errorStrategy 'ignore'
 
   input:

diff --git a/nextflow/ProteinFunction/nf_modules/sift.nf b/nextflow/ProteinFunction/nf_modules/sift.nf
@@ -31,7 +31,7 @@ process align_peptides {
 
   tag "${peptide.md5}"
   container "ensemblorg/sift:6.2.1"
-  memory '4 GB'
+  label 'medmem'
   errorStrategy 'ignore'
 
   input:
@@ -69,7 +69,7 @@ process run_sift_on_all_aminoacid_substitutions {
 
   tag "${peptide.md5}"
   container "ensemblorg/sift:6.2.1"
-  memory '4 GB'
+  label 'medmem'
   errorStrategy 'ignore'
   publishDir "${params.outdir}/sift"
 

diff --git a/nextflow/ProteinFunction/nf_modules/translations.nf b/nextflow/ProteinFunction/nf_modules/translations.nf
@@ -16,7 +16,7 @@ process translate_fasta {
 
   tag "${gtf} + ${fasta}"
   container "quay.io/biocontainers/agat:0.9.0--pl5321hdfd78af_0"
-  memory '20 GB'
+  label 'highmem'
   publishDir "${params.outdir}"
 
   input: