Fix publishing with trailing output directory name templates

CHANGELOG.md

@@ -4,6 +4,8 @@
 
 * `NextflowRunner`: Fix `readCsv` failing on S3 paths with Nextflow 25.10.x (PR #864). The `BufferedReader.ready()` method returns false for S3 streams when no data is pre-buffered, which broke compatibility with AWS SDK v2 used in Nextflow 25.10.x.
 
+* `Nextflowrunner`: fix publishing of directories when the output file name template contains a trailing slash (PR #867).
+
 # Viash 0.9.6 (2025-10-10): Hotfix for dependency path resolution
 
 This release fixes an issue with dependency resolution in some edge cases that was introduced in Viash 0.9.5.

src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf

@@ -39,10 +39,25 @@ process publishFilesProc {
   ]
     .transpose()
     .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
+      def infileString = infile.toString()
+      def outfileString = outfile.toString()
+      if (infileString != outfileString) {
+        /* Trailing slashes are removed from both the source and destination arguments.
+           From source arguments, this is useful when a source argument may have a trailing slash
+           and specify a symbolic link to a directory. Without removing the slash, cp will dereference
+           the symbolic link. 
+           See https://www.gnu.org/software/coreutils/manual/html_node/Trailing-slashes.html#Trailing-slashes-1
+
+           For the destination path addding a trailing slash is a problem when publishing directories: 
+           it requires the destination directory to exist. This fails because we only create the parent
+           directories first.
+        */
+        def regexTrailingSlashes = ~/\/+$/
+        def infileNoTrailingSlash = infileString - regexTrailingSlashes
+        def outfileNoTrailingSlash = outfileString - regexTrailingSlashes
         [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+          "[ -d \"\$(dirname '${outfileNoTrailingSlash}')\" ] || mkdir -p \"\$(dirname '${outfileNoTrailingSlash}')\"",
+          "cp -a '${infileNoTrailingSlash}' '${outfileNoTrailingSlash}'"
         ]
       } else {
         // no need to copy if infile is the same as outfile

src/test/resources/testnextflowvdsl3/src/output_directory/config.vsh.yaml

@@ -0,0 +1,15 @@
+name: output_directory
+arguments:
+  - name: "--output"
+    type: file
+    required: true
+    direction: output
+resources:
+  - type: bash_script
+    path: script.sh
+engines:
+  - type: native
+  - type: docker
+    image: nextflow/bash:latest
+runners:
+  - type: nextflow

src/test/resources/testnextflowvdsl3/src/output_directory/script.sh

@@ -0,0 +1,6 @@
+#!/bin/test
+
+[ -d "$par_output" ] && rm "$par_output"
+
+mkdir -p "$par_output"
+echo "test123" > "${par_output}/test1.txt"

src/test/scala/io/viash/runners/nextflow/Vdsl3StandaloneTest.scala

@@ -282,6 +282,28 @@ class Vdsl3StandaloneTest extends AnyFunSuite with BeforeAndAfterAll {
     }
   }
 
+    test("Output directory slashes", NextflowTest) {
+    val (exitCode, stdOut, stdErr) = NextflowTestHelper.run(
+      mainScript = "target/nextflow/output_directory/main.nf",
+      args = List(
+        "--output", "$id.$key.foo/",
+        "--publish_dir", "moduleOutputDir1"
+      ),
+      cwd = tempFolFile
+    )
+
+    assert(exitCode == 0, s"\nexit code was $exitCode\nStd output:\n$stdOut\nStd error:\n$stdErr")
+
+    val src = Source.fromFile(tempFolStr + "/moduleOutputDir1/run.output_directory.foo/test1.txt")
+
+    try {
+      val moduleOut = src.getLines().mkString(",")
+      assert(moduleOut.equals("test123"))
+    } finally {
+      src.close()
+    }
+  }
+
   override def afterAll(): Unit = {
     IO.deleteRecursively(temporaryFolder)
   }