Also check per process container when specifying '-with-docker' comma…

…nd line option. Fixes #39.
nextflow-io · Mar 26, 2015 · ea802f9 · ea802f9
1 parent 6b00962
commit ea802f9
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Showing 2 changed files with 60 additions and 1 deletion.
diff --git a/src/main/groovy/nextflow/script/ConfigBuilder.groovy b/src/main/groovy/nextflow/script/ConfigBuilder.groovy
@@ -323,7 +323,15 @@ class ConfigBuilder {
             }
 
             if( ! config.process.container ) {
-                throw new AbortOperationException("You request to run with Docker but no image has been specified")
+                def subProcs = config.process.findAll { it.key.startsWith('$') }
+                if ( ! subProcs )
+                    throw new AbortOperationException("You request to run with Docker but no image has been specified")
+                subProcs.each { name, value ->
+                    if ( ! value.container ) {
+                        throw new AbortOperationException("You request to run with Docker but no image has been specified")
+                    }
+                }
+
             }
         }
     }

diff --git a/src/test/groovy/nextflow/script/ConfigBuilderTest.groovy b/src/test/groovy/nextflow/script/ConfigBuilderTest.groovy
@@ -243,6 +243,57 @@ class ConfigBuilderTest extends Specification {
 
     }
 
+    def 'run with docker 3'() {
+        given:
+        def file = Files.createTempFile('test','config')
+        file.deleteOnExit()
+
+        when:
+        file.text =
+                '''
+                process.$test.container = 'busybox'
+                '''
+        def opt = new CliOptions(config: [file.toFile().canonicalPath])
+        def run = new CmdRun(withDocker: '-')
+        def config = new ConfigBuilder().setOptions(opt).setCmdRun(run).build()
+        then:
+        config.docker.enabled
+        config.process.$test.container == 'busybox'
+
+        when:
+        file.text =
+                '''
+                process.container = 'busybox'
+                '''
+        opt = new CliOptions(config: [file.toFile().canonicalPath])
+        run = new CmdRun(withDocker: '-')
+        config = new ConfigBuilder().setOptions(opt).setCmdRun(run).build()
+        then:
+        config.docker.enabled
+        config.process.container == 'busybox'
+
+        when:
+        opt = new CliOptions()
+        run = new CmdRun(withDocker: '-')
+        config = new ConfigBuilder().setOptions(opt).setCmdRun(run).build()
+        then:
+        def e = thrown(AbortOperationException)
+        e.message == 'You request to run with Docker but no image has been specified'
+
+        when:
+        file.text =
+                '''
+                process.$test.tag = 'tag'
+                '''
+        opt = new CliOptions(config: [file.toFile().canonicalPath])
+        run = new CmdRun(withDocker: '-')
+        config = new ConfigBuilder().setOptions(opt).setCmdRun(run).build()
+        then:
+        e = thrown(AbortOperationException)
+        e.message == 'You request to run with Docker but no image has been specified'
+
+    }
+
     def 'run without docker'() {
 
         given: