add resource limits

Author: TCLamnidis

conf/test_full.config

@@ -10,32 +10,13 @@
 ----------------------------------------------------------------------------------------
 */
 
-params {
-    config_profile_name           = 'Full test profile'
-    config_profile_description    = 'Full test dataset to check pipeline function'
-    pipelines_testdata_base_path  = 'https://raw.githubusercontent.com/TCLamnidis/test-datasets/'
-
-    // Input data for full size test
-    input                         = params.pipelines_testdata_base_path + 'eager/testdata/Benchmarking/eager3_benchmarking_vikingfish.tsv'
-
-    // Genome references
-    // Genome reference
-    fasta                         = 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_other/Gadus_morhua/reference/GCF_902167405.1_gadMor3.0/GCF_902167405.1_gadMor3.0_rna.fna.gz'
-
-    bwaalnn                       = 0.04
-    bwaalnl                       = 1024
-
-    run_bam_filtering             = true
-    bam_unmapped_type             = 'discard'
-    bam_mapping_quality_threshold = 25
-
-    run_genotyping                = true
-    genotyping_tool               = 'hc'
-    genotyping_source             = 'raw'
-    gatk_ploidy                   = 2
-}
-
 process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+    
     withName: FASTQC {
         cpus   = { 1                    }
         memory = { 15.GB * task.attempt }
@@ -69,3 +50,28 @@ process {
         time   = { 8.h   * task.attempt }
     }
 }
+
+params {
+    config_profile_name           = 'Full test profile'
+    config_profile_description    = 'Full test dataset to check pipeline function'
+    pipelines_testdata_base_path  = 'https://raw.githubusercontent.com/TCLamnidis/test-datasets/'
+
+    // Input data for full size test
+    input                         = params.pipelines_testdata_base_path + 'eager/testdata/Benchmarking/eager3_benchmarking_vikingfish.tsv'
+
+    // Genome references
+    // Genome reference
+    fasta                         = 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_other/Gadus_morhua/reference/GCF_902167405.1_gadMor3.0/GCF_902167405.1_gadMor3.0_rna.fna.gz'
+
+    bwaalnn                       = 0.04
+    bwaalnl                       = 1024
+
+    run_bam_filtering             = true
+    bam_unmapped_type             = 'discard'
+    bam_mapping_quality_threshold = 25
+
+    run_genotyping                = true
+    genotyping_tool               = 'hc'
+    genotyping_source             = 'raw'
+    gatk_ploidy                   = 2
+}