Added --config-working-dir to specify WORKDIR of the image (#12)

Signed-off-by: Paolo Di Tommaso <[email protected]>
Co-authored-by: Paolo Di Tommaso <[email protected]>

app/src/main/java/io/seqera/wavelit/App.java

@@ -106,6 +106,9 @@ public class App implements Runnable {
     @Option(names = {"--config-entrypoint"}, paramLabel = "''", description = "Overwrite the default ENTRYPOINT of the image.")
     private String entrypoint;
 
+    @Option(names = {"--config-working-dir"}, paramLabel = "''", description = "Overwrite the default WORKDIR of the image e.g. /some/work/dir.")
+    private String workingDir;
+
     @Option(names = {"--conda-file"}, paramLabel = "''", description = "A Conda file used to build the container e.g. /some/path/conda.yaml.")
     private String condaFile;
 
@@ -380,10 +383,16 @@ protected ContainerConfig prepareConfig() {
 
         // add the command if specified
         if( command != null ){
-            if( "".equals(command) ) throw new IllegalCliArgumentException("The specified command is an empty string");
+            if( "".equals(command.trim()) ) throw new IllegalCliArgumentException("The command cannot be an empty string");
             result.cmd = List.of(command);
         }
 
+        //add the working directory if specified
+        if( workingDir != null ){
+            if( "".equals(workingDir.trim()) ) throw new IllegalCliArgumentException("The working directory cannot be empty string");
+            result.workingDir = workingDir;
+        }
+
         // add the layers to the resulting config if specified
         if( layerDirs!=null ) for( String it : layerDirs ) {
             final Path loc = Path.of(it);

app/src/test/groovy/io/seqera/wavelit/AppTest.groovy

@@ -1,5 +1,6 @@
 package io.seqera.wavelit
 
+import java.nio.file.Files
 import java.time.Instant
 
 import io.seqera.wave.api.ContainerConfig
@@ -86,6 +87,35 @@ class AppTest extends Specification {
 
     }
 
+    def "test valid working directory"() {
+        given:
+        def app = new App()
+        String[] args = ["--config-working-dir", "/work/dir"]
+
+        when:
+        new CommandLine(app).parseArgs(args)
+        then:
+        app.@workingDir == "/work/dir"
+
+        when:
+        def config = app.prepareConfig()
+        then:
+        config == new ContainerConfig(workingDir: '/work/dir')
+    }
+
+    def "test invalid working directory"() {
+        given:
+        def app = new App()
+        String[] args = ["--config-working-dir", "  "]
+
+        when:
+        new CommandLine(app).parseArgs(args)
+        app.prepareConfig()
+        then:
+        thrown(IllegalCliArgumentException)
+
+    }
+
     def 'should dump response to yaml' () {
         given:
         def app = new App()