Use -1 as default for *_fix_cpus int params

main.nf

@@ -143,15 +143,15 @@ if (params.coassemble_group && params.binning_map_mode == 'own')
     exit 1, "Invalid combination of parameter '--binning_map_mode own' and parameter '--coassemble_group'. Select either 'all' or 'group' mapping mode when performing group-wise co-assembly."
 
 // Check if specified cpus for SPAdes are available
-if ( params.spades_fix_cpus && params.spades_fix_cpus > params.max_cpus )
+if ( params.spades_fix_cpus > params.max_cpus )
     exit 1, "Invalid parameter '--spades_fix_cpus ${params.spades_fix_cpus}', max cpus are '${params.max_cpus}'."
-if ( params.spadeshybrid_fix_cpus && params.spadeshybrid_fix_cpus > params.max_cpus )
+if ( params.spadeshybrid_fix_cpus > params.max_cpus )
     exit 1, "Invalid parameter '--spadeshybrid_fix_cpus ${params.spadeshybrid_fix_cpus}', max cpus are '${params.max_cpus}'."
 // Check if settings concerning reproducibility of used tools are consistent and print warning if not
-if (params.megahit_fix_cpu_1 || params.spades_fix_cpus || params.spadeshybrid_fix_cpus){
-    if (!params.skip_spades && !params.spades_fix_cpus)
+if (params.megahit_fix_cpu_1 || params.spades_fix_cpus != -1 || params.spadeshybrid_fix_cpus != -1){
+    if (!params.skip_spades && params.spades_fix_cpus == -1)
         log.warn "At least one assembly process is run with a parameter to ensure reproducible results, but SPAdes not. Consider using the parameter '--spades_fix_cpus'."
-    if (hybrid && !params.skip_spadeshybrid && !params.spadeshybrid_fix_cpus)
+    if (hybrid && params.skip_spadeshybrid && params.spadeshybrid_fix_cpus == -1)
         log.warn "At least one assembly process is run with a parameter to ensure reproducible results, but SPAdes hybrid not. Consider using the parameter '--spadeshybrid_fix_cpus'."
     if (!params.skip_megahit && !params.megahit_fix_cpu_1)
         log.warn "At least one assembly process is run with a parameter to ensure reproducible results, but MEGAHIT not. Consider using the parameter '--megahit_fix_cpu_1'."

modules/local/spades.nf

@@ -32,7 +32,7 @@ process SPADES {
     script:
     def software = getSoftwareName(task.process)
     maxmem = task.memory.toGiga()
-    if ( !params.spades_fix_cpus || task.cpus == params.spades_fix_cpus )
+    if ( params.spades_fix_cpus == -1 || task.cpus == params.spades_fix_cpus )
         """
         metaspades.py \
             ${params.spades_options} \

modules/local/spadeshybrid.nf

@@ -32,7 +32,7 @@ process SPADESHYBRID {
     script:
     def software = getSoftwareName(task.process)
     maxmem = task.memory.toGiga()
-    if ( !params.spadeshybrid_fix_cpus || task.cpus == params.spadeshybrid_fix_cpus )
+    if ( params.spadeshybrid_fix_cpus == -1 || task.cpus == params.spadeshybrid_fix_cpus )
         """
         metaspades.py \
             ${params.spades_options} \

nextflow.config

@@ -62,8 +62,8 @@ params {
 
   // Reproducibility options
   megahit_fix_cpu_1          = false
-  spades_fix_cpus            = false
-  spadeshybrid_fix_cpus      = false
+  spades_fix_cpus            = -1
+  spadeshybrid_fix_cpus      = -1
   metabat_rng_seed           = 1
 
   // References
@@ -226,10 +226,10 @@ def check_megahit_cpus (x, attempt ) {
   else return check_max (x * attempt, 'cpus' )
 }
 def check_spades_cpus (x, attempt ) {
-  if (params.spades_fix_cpus) return check_max (params.spades_fix_cpus, 'cpus' )
+  if (params.spades_fix_cpus != -1) return check_max (params.spades_fix_cpus, 'cpus' )
   else return check_max (x * attempt, 'cpus' )
 }
 def check_spadeshybrid_cpus (x, attempt ) {
-  if (params.spadeshybrid_fix_cpus) return check_max (params.spadeshybrid_fix_cpus, 'cpus' )
+  if (params.spadeshybrid_fix_cpus != -1) return check_max (params.spadeshybrid_fix_cpus, 'cpus' )
   else return check_max (x * attempt, 'cpus' )
 }

nextflow_schema.json

@@ -250,13 +250,15 @@
                 },
                 "spades_fix_cpus": {
                     "type": "integer",
+                    "default": -1,
                     "description": "Fix number of CPUs used by SPAdes. Not increased with retries.",
-                    "help_text": "SPAdes is designed to be deterministic for a given number of threads. To generate reproducible results fix the number of CPUs using this parameter.\n\nWhen using this parameter do not change the number of CPUs for the `spades` process with a custom config file. This would result in an error.\n\nDefault: The number of CPUs is specified in the `base.config` file, and increased with each retry."
+                    "help_text": "SPAdes is designed to be deterministic for a given number of threads. To generate reproducible results fix the number of CPUs using this parameter.\n\nWhen using this parameter do not change the number of CPUs for the `spades` process with a custom config file. This would result in an error.\n\nDefault: -1 (the number of CPUs is specified in the `base.config` or in a custom config file, and increased with each retry)."
                 },
                 "spadeshybrid_fix_cpus": {
                     "type": "integer",
+                    "default": -1,
                     "description": "Fix number of CPUs used by SPAdes hybrid. Not increased with retries.",
-                    "help_text": "SPAdes is designed to be deterministic for a given number of threads. To generate reproducible results fix the number of CPUs using this parameter.\n\nWhen using this parameter do not change the number of CPUs for the `spadeshybrid` process with a custom config file. This would result in an error.\n\nDefault: The number of CPUs is specified in the `base.config` file, and increased with each retry."
+                    "help_text": "SPAdes is designed to be deterministic for a given number of threads. To generate reproducible results fix the number of CPUs using this parameter.\n\nWhen using this parameter do not change the number of CPUs for the `spadeshybrid` process with a custom config file. This would result in an error.\n\nDefault: -1 (the number of CPUs is specified in the `base.config` or in a custom config file, and increased with each retry)."
                 },
                 "metabat_rng_seed": {
                     "type": "integer",