From 045dd971ac8718cca877dedd41c77e128a5d1c64 Mon Sep 17 00:00:00 2001
From: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Mon, 23 Oct 2023 15:02:13 +0200
Subject: [PATCH 1/2] Using a nextflow module with the same name as a nextflow
 operator causes recursion.

---
 .../src/concat/config.vsh.yaml                | 20 +++++++++++++
 .../testnextflowvdsl3/src/concat/script.sh    |  1 +
 .../operator_conflict/config.vsh.yaml         | 13 ++++++++
 .../src/test_wfs/operator_conflict/main.nf    | 30 +++++++++++++++++++
 4 files changed, 64 insertions(+)
 create mode 100644 src/test/resources/testnextflowvdsl3/src/concat/config.vsh.yaml
 create mode 100644 src/test/resources/testnextflowvdsl3/src/concat/script.sh
 create mode 100644 src/test/resources/testnextflowvdsl3/src/test_wfs/operator_conflict/config.vsh.yaml
 create mode 100644 src/test/resources/testnextflowvdsl3/src/test_wfs/operator_conflict/main.nf

diff --git a/src/test/resources/testnextflowvdsl3/src/concat/config.vsh.yaml b/src/test/resources/testnextflowvdsl3/src/concat/config.vsh.yaml
new file mode 100644
index 000000000..2666064af
--- /dev/null
+++ b/src/test/resources/testnextflowvdsl3/src/concat/config.vsh.yaml
@@ -0,0 +1,20 @@
+functionality:
+  name: concat
+  arguments:
+    - name: "--input"
+      type: file
+      required: true
+      example: input.txt
+    - name: "--output"
+      type: file
+      required: true
+      direction: output
+      example: output.txt
+  resources:
+    - type: bash_script
+      path: script.sh
+platforms:
+  - type: native
+  - type: docker
+    image: nextflow/bash:latest
+  - type: nextflow
diff --git a/src/test/resources/testnextflowvdsl3/src/concat/script.sh b/src/test/resources/testnextflowvdsl3/src/concat/script.sh
new file mode 100644
index 000000000..d626016cc
--- /dev/null
+++ b/src/test/resources/testnextflowvdsl3/src/concat/script.sh
@@ -0,0 +1 @@
+cp "$par_input" "$par_output"
\ No newline at end of file
diff --git a/src/test/resources/testnextflowvdsl3/src/test_wfs/operator_conflict/config.vsh.yaml b/src/test/resources/testnextflowvdsl3/src/test_wfs/operator_conflict/config.vsh.yaml
new file mode 100644
index 000000000..c09eae976
--- /dev/null
+++ b/src/test/resources/testnextflowvdsl3/src/test_wfs/operator_conflict/config.vsh.yaml
@@ -0,0 +1,13 @@
+functionality:
+  name: operator_conflict
+  namespace: test_wfs
+  resources:
+    - type: nextflow_script
+      path: main.nf
+      entrypoint: base
+    # TODO: make absolute when the ns build uses the right CWD
+    - path: ../../../resources
+  dependencies:
+    - name: concat
+platforms:
+  - type: nextflow
\ No newline at end of file
diff --git a/src/test/resources/testnextflowvdsl3/src/test_wfs/operator_conflict/main.nf b/src/test/resources/testnextflowvdsl3/src/test_wfs/operator_conflict/main.nf
new file mode 100644
index 000000000..4099a20aa
--- /dev/null
+++ b/src/test/resources/testnextflowvdsl3/src/test_wfs/operator_conflict/main.nf
@@ -0,0 +1,30 @@
+
+workflow base {
+  take: input_ch
+  main:
+
+  // generate list from 0 to 1
+  ch = Channel.fromList(0..1)
+    | map { num ->
+      // create temporary file
+      file = tempFile()
+      file.write("num: $num")
+
+      ["num$num", [ num: num, file: file ]]
+    }
+    | concat.run(
+      fromState: ["input": "input"],
+      toState: {id, output, state -> 
+        def newState = [
+          "step1_output": output.output, 
+          "num": state.num,
+          "file": state.file
+        ]
+        return newState
+      }
+    )
+    
+
+  emit:
+  input_ch
+}

From 438211451881849f6020e56a6c93c467e9aebb06 Mon Sep 17 00:00:00 2001
From: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Mon, 23 Oct 2023 15:19:59 +0200
Subject: [PATCH 2/2] Add test to sbt

---
 .../viash/runners/nextflow/NextflowScriptTest.scala  | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/src/test/scala/io/viash/runners/nextflow/NextflowScriptTest.scala b/src/test/scala/io/viash/runners/nextflow/NextflowScriptTest.scala
index 4db43d0b1..cb8f1689a 100644
--- a/src/test/scala/io/viash/runners/nextflow/NextflowScriptTest.scala
+++ b/src/test/scala/io/viash/runners/nextflow/NextflowScriptTest.scala
@@ -122,6 +122,18 @@ class NextflowScriptTest extends AnyFunSuite with BeforeAndAfterAll {
     assert(exitCode == 0, s"\nexit code was $exitCode\nStd output:\n$stdOut\nStd error:\n$stdErr")
   }
 
+  test("Test conflicts with nextlow operator", DockerTest, NextflowTest) {
+    val (exitCode, stdOut, stdErr) = NextflowTestHelper.run(
+      mainScript = "target/nextflow/test_wfs/operator_conflict/main.nf",
+      args = List(
+        "--publish_dir", "output"
+      ),
+      cwd = tempFolFile
+    )
+
+    assert(exitCode == 0, s"\nexit code was $exitCode\nStd output:\n$stdOut\nStd error:\n$stdErr")
+  }
+
 
   test("Test nested workflows", DockerTest, NextflowTest) {
     val (exitCode, stdOut, stdErr) = NextflowTestHelper.run(