analysis: change workflow docker, #TASK-6445

opencb · Sep 30, 2024 · 14e6b6b · 14e6b6b
1 parent d74a555
commit 14e6b6b
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Showing 2 changed files with 19 additions and 4 deletions.
diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/workflow/NextFlowExecutor.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/workflow/NextFlowExecutor.java
@@ -267,7 +267,7 @@ protected void run() throws Exception {
         // Build output binding
         AbstractMap.SimpleEntry<String, String> outputBinding = new AbstractMap.SimpleEntry<>(outDirPath, outDirPath);
 
-        String dockerImage = "opencb/opencga-workflow";
+        String dockerImage = "opencb/opencga-workflow:TASK-6445";
         StringBuilder stringBuilder = new StringBuilder()
                 .append("bash -c \"NXF_VER=").append(workflow.getManager().getVersion()).append(" nextflow -c ").append(nextflowConfigPath).append(" run ");
         if (workflow.getRepository() != null && StringUtils.isNotEmpty(workflow.getRepository().getImage())) {

diff --git a/opencga-analysis/src/test/java/org/opencb/opencga/analysis/tools/WorkflowExecutorTest.java b/opencga-analysis/src/test/java/org/opencb/opencga/analysis/tools/WorkflowExecutorTest.java
@@ -21,6 +21,7 @@
 import java.io.InputStream;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
@@ -83,6 +84,20 @@ public void nextflowDockerTest() throws ToolException, CatalogException, IOExcep
         WorkflowCreateParams workflow = new WorkflowCreateParams()
                 .setId("workflow")
                 .setType(Workflow.Type.OTHER)
+                .setVariables(Arrays.asList(
+                        new WorkflowVariable()
+                                .setId("outdir")
+                                .setOutput(true)
+                                .setRequired(true),
+                        new WorkflowVariable()
+                                .setId("genome")
+                                .setRequired(true)
+                                .setDefaultValue("GRCh37"),
+                        new WorkflowVariable()
+                                .setId("-profile")
+                                .setRequired(true)
+                                .setDefaultValue("docker")
+                ))
                 .setRepository(new WorkflowRepository("nf-core/demo"));
         catalogManager.getWorkflowManager().create(studyFqn, workflow.toWorkflow(), QueryOptions.empty(), ownerToken);
 
@@ -99,9 +114,9 @@ public void nextflowDockerTest() throws ToolException, CatalogException, IOExcep
         NextFlowExecutor nextFlowExecutorTest = new NextFlowExecutor();
         Map<String, String> cliParams = new HashMap<>();
         cliParams.put("input", "file://samplesheet.csv");
-        cliParams.put("outdir", "$OUTPUT");
-        cliParams.put("genome", "GRCh37");
-        cliParams.put("-profile", "docker");
+//        cliParams.put("outdir", "$OUTPUT");
+//        cliParams.put("genome", "GRCh37");
+//        cliParams.put("-profile", "docker");
         NextFlowRunParams runParams = new NextFlowRunParams(workflow.getId(), 1, cliParams);
         ObjectMap params = runParams.toObjectMap();
         params.put(ParamConstants.STUDY_PARAM, studyFqn);