Add initial support for bin in working directory

Signed-off-by: Liam Beckman <lbeckman314@gmail.com>
nextflow-io · Dec 21, 2023 · 0f36a79 · 0f36a79
1 parent c46fa3a
commit 0f36a79
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Showing 2 changed files with 14 additions and 3 deletions.
diff --git a/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/executor/TesFileCopyStrategy.groovy b/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/executor/TesFileCopyStrategy.groovy
@@ -113,7 +113,8 @@ class TesFileCopyStrategy implements ScriptFileCopyStrategy {
             copy.remove('PATH')
         // when a remote bin directory is provide managed it properly
         if( remoteBinDir ) {
-            result << "cp -r ${remoteBinDir}/* \$PWD/nextflow-bin/\n"
+            result << "mkdir -p \$PWD/nextflow-bin/\n"
+            result << "cp -r \$PWD/bin/* \$PWD/nextflow-bin/\n"
             result << "chmod +x \$PWD/nextflow-bin/* || true\n"
             result << "export PATH=\$PWD/nextflow-bin:\$PATH\n"
         }

diff --git a/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/executor/TesTaskHandler.groovy b/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/executor/TesTaskHandler.groovy
@@ -23,6 +23,7 @@ import static nextflow.processor.TaskStatus.COMPLETED
 import static nextflow.processor.TaskStatus.RUNNING
 
 import java.nio.file.Path
+import java.nio.file.Files
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
@@ -189,6 +190,10 @@ class TesTaskHandler extends TaskHandler {
         // add task control files
         body.addInputsItem(inItem(scriptFile))
         body.addInputsItem(inItem(wrapperFile))
+        Path remoteBinDir = executor.getRemoteBinDir()
+        Files.newDirectoryStream(remoteBinDir).each { path ->
+            body.addInputsItem(inItem(path, null ,true))
+        }
 
         // add task input files
         if(inputFile.exists()) body.addInputsItem(inItem(inputFile))
@@ -234,10 +239,15 @@ class TesTaskHandler extends TaskHandler {
         return size != null ? ((double)size.bytes)/1073741824 : null
     }
 
-    private TesInput inItem( Path realPath, String fileName = null) {
+    private TesInput inItem( Path realPath, String fileName = null, boolean isBin = false) {
         def result = new TesInput()
         result.url = realPath.toUriString()
-        result.path = fileName ? "$WORK_DIR/$fileName" : "$WORK_DIR/${realPath.getName()}"
+        if (isBin) {
+            result.path = fileName ? "$WORK_DIR/bin/$fileName" : "$WORK_DIR/bin/${realPath.getName()}"
+        }
+        else {
+            result.path = fileName ? "$WORK_DIR/$fileName" : "$WORK_DIR/${realPath.getName()}"
+        }
         log.trace "[TES] Adding INPUT file: $result"
         return result
     }