Parameter to give more memory to assemblyscan.

oist · Oct 29, 2024 · 221ea9d · 221ea9d
1 parent d01b98c
commit 221ea9d
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Showing 3 changed files with 14 additions and 2 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -30,7 +30,7 @@ process {
     }
     withLabel:process_low {
         cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
+        memory = { check_max( params.memory * task.attempt, 'memory'  ) }
         time   = { check_max( 1.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_medium {

diff --git a/nextflow.config b/nextflow.config
@@ -12,6 +12,9 @@ params {
     // Input options
     input                      = null
 
+    // Performance options
+    memory                     = '6.GB'
+
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
@@ -227,7 +230,7 @@ manifest {
     description     = """Download and pre-process genomes for the Scrambling in the Tree of Life project"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '3.0.0'
+    version         = '4.0.0'
     doi             = ''
 }
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -105,6 +105,15 @@
                     "hidden": true,
                     "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
                 },
+                "memory": {
+                    "type": "string",
+                    "description": "Memory given to ASSEMBLYSCAN.",
+                    "default": "6.GB",
+                    "fa_icon": "fas fa-memory",
+                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
+                    "hidden": true,
+                    "help_text": "Use to set the memory requirement of the ASSEMBLYSCAN process (the only process_low at the moment). Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
+                },
                 "max_memory": {
                     "type": "string",
                     "description": "Maximum amount of memory that can be requested for any single job.",