Changin PERL version string and Updating executor values

sanger-tol · Dec 9, 2024 · 3c15e2d · 3c15e2d
1 parent 2764466
commit 3c15e2d
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Showing 4 changed files with 6 additions and 20 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -133,7 +133,7 @@ process {
     }
 
     withName: PRETEXTMAP_STANDRD {
-        ext.args        = { "${meta.map_order.equals("length") ? "--sortby length": "--sortby nosort" } --mapq 0 --memory ${task.memory.giga}" }
+        ext.args        = { "${meta.map_order.equals("length") ? "--sortby length": "--sortby nosort" } --mapq 0" }
         ext.prefix      = { "${meta.id}_normal_pi" }
     }
 

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -12,23 +12,16 @@
 
 cleanup = true
 
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '10.GB',
-        time: '1.h'
-    ]
-}
+executor.cpus = 50
+executor.memory = 50.GB
+executor.time = 1.h
 
 params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
     // Limit resources so that this can run on GitHub Actions
-    max_cpus    = 1
-    max_memory  = '10.GB'
-    max_time    = '6.h'
 
     sample      = "testing"
     input       = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValTinyData/assembly/draft/grTriPseu1.fa"

diff --git a/modules/local/extract_repeat.nf b/modules/local/extract_repeat.nf
@@ -25,7 +25,7 @@ process EXTRACT_REPEAT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1 | grep -oP '\(\K[^\)]+')
+        perl: \$(echo \$(perl --version 2>&1) | awk '/This/ {print \$9}') | tr -d ())
         extract_repeat.pl: $VERSION
     END_VERSIONS
     """
@@ -38,7 +38,7 @@ process EXTRACT_REPEAT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1 | grep -oP '\(\K[^\)]+')
+        perl: \$(echo \$(perl --version 2>&1) | awk '/This/ {print \$9}') | tr -d ())
         extract_repeat.pl: $VERSION
     END_VERSIONS
     """

diff --git a/nextflow.config b/nextflow.config
@@ -42,13 +42,6 @@ params {
     config_profile_url         = null
     config_profile_name        = null
 
-
-    // Max resource options
-    // Defaults only, expecting to be overwritten
-    max_memory                 = '128.GB'
-    max_cpus                   = 16
-    max_time                   = '240.h'
-
 }
 
 // Load base.config by default for all pipelines