diff --git a/seda-plugin-cga/src/main/java/org/sing_group/seda/cga/cli/CgaPipelineCommand.java b/seda-plugin-cga/src/main/java/org/sing_group/seda/cga/cli/CgaPipelineCommand.java index 6545b83d..7a8e477a 100644 --- a/seda-plugin-cga/src/main/java/org/sing_group/seda/cga/cli/CgaPipelineCommand.java +++ b/seda-plugin-cga/src/main/java/org/sing_group/seda/cga/cli/CgaPipelineCommand.java @@ -23,7 +23,9 @@ import static java.util.Arrays.asList; import static java.util.Collections.emptyList; +import static java.util.Collections.emptyMap; import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.DESCRIPTION; +import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.GROUP; import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.NAME; import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_CGA_RESULTS_HELP; import static org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo.PARAM_CGA_RESULTS_NAME; @@ -59,7 +61,6 @@ import java.io.File; import java.io.IOException; -import java.util.Collections; import java.util.List; import java.util.Map; import java.util.Optional; @@ -67,7 +68,6 @@ import org.sing_group.seda.cga.execution.CgaBinariesExecutor; import org.sing_group.seda.cga.execution.CgaCompiPipelineConfiguration; import org.sing_group.seda.cga.execution.DefaultDockerCgaBinariesExecutor; -import org.sing_group.seda.cga.plugin.core.CgaPipelineSedaPluginInfo; import org.sing_group.seda.cga.transformation.dataset.CgaResults; import org.sing_group.seda.cga.transformation.provider.CgaPipelineTransformationProvider; import org.sing_group.seda.cli.ExternalSoftwareExecutionCommand; @@ -144,7 +144,9 @@ public class CgaPipelineCommand extends ExternalSoftwareExecutionCommand { public static final StringOption OPTION_DOCKER_MODE = new StringOption( - PARAM_DOCKER_MODE_NAME, PARAM_DOCKER_MODE_SHORT_NAME, PARAM_DOCKER_MODE_HELP, true, true + SOFTWARE_EXECUTION_CATEGORY, + PARAM_DOCKER_MODE_NAME, PARAM_DOCKER_MODE_SHORT_NAME, PARAM_DOCKER_MODE_HELP, + true, true ); @Override @@ -164,12 +166,12 @@ public String getDescription() { @Override protected String getSedaGroup() { - return CgaPipelineSedaPluginInfo.GROUP; + return GROUP; } @Override protected Map, String> getLocalOptionsToEnablePropertyMap() { - return Collections.emptyMap(); + return emptyMap(); } @Override