Allow boolean params to implicitly default to false (#6764)

Author: bentsherman

docs/workflow.md

@@ -49,7 +49,7 @@ params {
     input: Path
 
     // Whether to save intermediate files.
-    save_intermeds: Boolean = false
+    save_intermeds: Boolean
 }
 ```
 
@@ -69,7 +69,7 @@ As a best practice, parameters should only be referenced in the entry workflow o
 
 The default value can be overridden by the command line, params file, or config file. Parameters from multiple sources are resolved in the order described in {ref}`cli-params`. Parameters specified on the command line are converted to the appropriate type based on the corresponding type annotation.
 
-A parameter that doesn't specify a default value is a *required* parameter. If a required parameter is not given a value at runtime, the run will fail.
+A parameter that doesn't specify a default value is a *required* parameter. If a required parameter is not given a value at runtime, the run will fail. Boolean parameters that don't specify a default value default to `false`.
 
 :::{versionadded} 26.04.0
 :::

modules/nextflow/src/main/groovy/nextflow/script/ParamsDsl.groovy

@@ -46,6 +46,8 @@ class ParamsDsl {
     private Map<String,Param> declarations = [:]
 
     void declare(String name, Class type, boolean optional, Object defaultValue = null) {
+        if( defaultValue == null && type == Boolean )
+            defaultValue = false
         declarations[name] = new Param(name, type, optional, defaultValue)
     }
 

modules/nextflow/src/test/groovy/nextflow/script/ParamsDslTest.groovy

@@ -26,7 +26,7 @@ class ParamsDslTest extends Specification {
         def dsl = new ParamsDsl()
         dsl.declare('input', Path, false)
         dsl.declare('chunk_size', Integer, false, 1)
-        dsl.declare('save_intermeds', Boolean, false, false)
+        dsl.declare('save_intermeds', Boolean, false)
         dsl.apply(session)
         then:
         session.binding.getParams() == [input: FileHelper.asPath('./data'), chunk_size: 3, save_intermeds: false, outdir: 'results']
@@ -55,7 +55,7 @@ class ParamsDslTest extends Specification {
         when:
         def dsl = new ParamsDsl()
         dsl.declare('input', Path, false)
-        dsl.declare('save_intermeds', Boolean, false, false)
+        dsl.declare('save_intermeds', Boolean, false)
         dsl.apply(session)
         then:
         def e = thrown(ScriptRuntimeException)
@@ -72,7 +72,7 @@ class ParamsDslTest extends Specification {
         when:
         def dsl = new ParamsDsl()
         dsl.declare('input', Path, false)
-        dsl.declare('save_intermeds', Boolean, false, false)
+        dsl.declare('save_intermeds', Boolean, false)
         dsl.apply(session)
         then:
         def e = thrown(ScriptRuntimeException)
@@ -89,7 +89,7 @@ class ParamsDslTest extends Specification {
         when:
         def dsl = new ParamsDsl()
         dsl.declare('input', Path, false)
-        dsl.declare('save_intermeds', Boolean, false, false)
+        dsl.declare('save_intermeds', Boolean, false)
         dsl.apply(session)
         then:
         def e = thrown(ScriptRuntimeException)

tests/checks/params-dsl.nf/.checks

@@ -5,6 +5,7 @@ $NXF_RUN --input ./data > stdout
 
 < stdout grep -F 'params.input = [./data]'
 < stdout grep -F 'params.save_intermeds = false'
+< stdout grep -F 'params.method = auto'
 
 echo
 echo "Test missing required param"
@@ -17,13 +18,23 @@ set -e
 
 < stdout grep -F 'Parameter `input` is required'
 
+echo
+echo "Test overwrite script param from command line"
+echo
+$NXF_RUN -c ../../params-dsl.config --input 'alpha,beta' --save_intermeds --method special > stdout
+
+< stdout grep -F 'params.input = [alpha, beta]'
+< stdout grep -F 'params.save_intermeds = true'
+< stdout grep -F 'params.method = special'
+
 echo
 echo "Test overwrite script param from config profile"
 echo
 $NXF_RUN -c ../../params-dsl.config -profile test > stdout
 
 < stdout grep -F 'params.input = [alpha, beta, delta]'
 < stdout grep -F 'params.save_intermeds = true'
+< stdout grep -F 'params.method = special'
 
 echo
 echo "Test invalid param"

tests/params-dsl.config

@@ -5,5 +5,6 @@ profiles {
     test {
         params.input = 'alpha,beta,delta'
         params.save_intermeds = true
+        params.method = 'special'
     }
 }

tests/params-dsl.nf

@@ -16,15 +16,19 @@
  */
 
 params {
-  // List of IDs.
+  // Comma-separated list of IDs.
   input: String
 
   // Whether to save intermediate outputs.
-  save_intermeds: Boolean = false
+  save_intermeds: Boolean
+
+  // Method to use for analyzing samples.
+  method: String = 'auto'
 }
 
 workflow {
   main:
   println "params.input = ${params.input.tokenize(',')}"
   println "params.save_intermeds = ${params.save_intermeds}"
+  println "params.method = ${params.method}"
 }