Add fallback command for micromamba

modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy

@@ -285,7 +285,8 @@ class CondaCache {
         def cmd
         if( isYamlFilePath(condaEnv) ) {
             final target = isYamlUriPath(condaEnv) ? condaEnv : Escape.path(makeAbsolute(condaEnv))
-            cmd = "${binaryName} env create --prefix ${Escape.path(prefixPath)} --file ${target}"
+            final yesOpt = binaryName == 'micromamba' ? '--yes ' : ''
+            cmd = "${binaryName} env create ${yesOpt}--prefix ${Escape.path(prefixPath)} --file ${target}"
         }
         else if( isTextFilePath(condaEnv) ) {
             cmd = "${binaryName} create ${opts}--yes --quiet --prefix ${Escape.path(prefixPath)} --file ${Escape.path(makeAbsolute(condaEnv))}"

modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy

@@ -533,10 +533,13 @@ class BashWrapperBuilder {
     private String getCondaActivateSnippet() {
         if( !condaEnv )
             return null
-        def result = "# conda environment\n"
-        result += 'source $(conda info --json | awk \'/conda_prefix/ { gsub(/"|,/, "", $2); print $2 }\')'
-        result += "/bin/activate ${Escape.path(condaEnv)}\n"
-        return result
+        def command = 'source $(conda info --json | awk \'/conda_prefix/ { gsub(/"|,/, "", $2); print $2 }\')/bin/activate'
+        if( condaConfig && condaConfig.useMicromamba() )
+            command = 'eval "$(micromamba shell hook --shell bash)" && micromamba activate'
+        return """\
+            # conda environment
+            ${command} ${Escape.path(condaEnv)}
+            """.stripIndent()
     }
 
     private String getSpackActivateSnippet() {

modules/nextflow/src/main/groovy/nextflow/processor/TaskBean.groovy

@@ -16,6 +16,8 @@
 
 package nextflow.processor
 
+import nextflow.conda.CondaConfig
+
 import java.nio.file.Path
 
 import groovy.transform.CompileStatic
@@ -48,6 +50,8 @@ class TaskBean implements Serializable, Cloneable {
 
     Path condaEnv
 
+    CondaConfig condaConfig
+
     Path spackEnv
 
     List<String> moduleNames
@@ -131,6 +135,7 @@ class TaskBean implements Serializable, Cloneable {
         this.environment = task.getEnvironment()
 
         this.condaEnv = task.getCondaEnv()
+        this.condaConfig = task.getCondaConfig()
         this.spackEnv = task.getSpackEnv()
         this.moduleNames = task.config.getModule()
         this.shell = task.config.getShell() ?: BashWrapperBuilder.BASH

modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy

@@ -16,6 +16,8 @@
 
 package nextflow.processor
 
+import nextflow.conda.CondaConfig
+
 import java.nio.file.FileSystems
 import java.nio.file.NoSuchFileException
 import java.nio.file.Path
@@ -967,5 +969,9 @@ class TaskRun implements Cloneable {
     TaskBean toTaskBean() {
         return new TaskBean(this)
     }
+
+    CondaConfig getCondaConfig() {
+        return processor.session.getCondaConfig()
+    }
 }
 

modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy

@@ -16,6 +16,8 @@
 
 package nextflow.executor
 
+import nextflow.conda.CondaConfig
+
 import java.nio.file.FileSystemException
 import java.nio.file.Files
 import java.nio.file.Path
@@ -775,13 +777,20 @@ class BashWrapperBuilderTest extends Specification {
 
         when:
         def CONDA = Paths.get('/some/conda/env/foo')
-        binding = newBashWrapperBuilder(condaEnv: CONDA).makeBinding()
+        def config = new CondaConfig(['useMicromamba': MICROMAMBA])
+        binding = newBashWrapperBuilder(condaEnv: CONDA, condaConfig: config).makeBinding()
         then:
-        binding.conda_activate == '''\
+        binding.conda_activate == RESULT
+        where:
+        MICROMAMBA | RESULT
+        false      | '''\
                 # conda environment
-                source $(conda info --json | awk '/conda_prefix/ { gsub(/"|,/, "", $2); print $2 }')/bin/activate /some/conda/env/foo
+                source $(conda info --json | awk \'/conda_prefix/ { gsub(/"|,/, "", $2); print $2 }\')/bin/activate /some/conda/env/foo
+                '''.stripIndent()
+        true       | '''\
+                # conda environment
+                eval "$(micromamba shell hook --shell bash)" && micromamba activate /some/conda/env/foo
                 '''.stripIndent()
-
     }
 
     def 'should create spack activate snippet' () {