From cee7fd00b680dabccec32384ff9b15e942993ac7 Mon Sep 17 00:00:00 2001
From: Stephen Kelly <stevekm@users.noreply.github.com>
Date: Mon, 25 Mar 2024 12:28:08 -0400
Subject: [PATCH 1/2] merge nextflow.config files and add exec test case in
 test workflow

---
 nextflow.config       | 24 ------------------------
 tests/nextflow.config | 26 ++++++++++++++++++++++++++
 tests/test.nf         | 23 +++++++++++++++++++----
 3 files changed, 45 insertions(+), 28 deletions(-)
 delete mode 100644 nextflow.config

diff --git a/nextflow.config b/nextflow.config
deleted file mode 100644
index 6219b1b..0000000
--- a/nextflow.config
+++ /dev/null
@@ -1,24 +0,0 @@
-plugins {
-    id 'nf-prov'
-}
-
-params {
-    outdir = 'results'
-}
-
-prov {
-    formats {
-        bco {
-            file = "${params.outdir}/bco.json"
-            overwrite = true
-        }
-        dag {
-            file = "${params.outdir}/dag.html"
-            overwrite = true
-        }
-        legacy {
-            file = "${params.outdir}/manifest.json"
-            overwrite = true
-        }
-    }
-}
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 3044716..c18d0bb 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -1,3 +1,29 @@
+plugins {
+    id 'nf-prov'
+}
+
+params {
+    outdir = "results"
+    constant = "foo"
+}
+
+prov {
+    formats {
+        bco {
+            file = "${params.outdir}/bco.json"
+            overwrite = true
+        }
+        dag {
+            file = "${params.outdir}/dag.html"
+            overwrite = true
+        }
+        legacy {
+            file = "${params.outdir}/manifest.json"
+            overwrite = true
+        }
+    }
+}
+
 manifest {
     name = "nf-prov-test"
     author = "Bruno Grande"
diff --git a/tests/test.nf b/tests/test.nf
index 4e050cd..d2edacc 100644
--- a/tests/test.nf
+++ b/tests/test.nf
@@ -1,10 +1,8 @@
 nextflow.enable.dsl=2
 
-params.constant = "foo"
-
 process RNG {
-
-    publishDir "results", mode: 'copy'
+    tag "${prefix}"
+    publishDir "${params.outdir}", mode: 'copy'
 
     input:
     tuple val(prefix), val(constant)
@@ -21,10 +19,27 @@ process RNG {
 
 }
 
+// shows nf-prov behavior with exec tasks
+process EXEC_FOO {
+    tag "${prefix}"
+    publishDir "${params.outdir}", mode: 'copy'
+
+    input:
+    tuple val(prefix), val(constant)
+
+    output:
+    path(outputfile)
+
+    exec:
+    outputfile = new File("${task.workDir}/${prefix}.exec_foo.txt")
+    outputfile.write(prefix)
+}
+
 workflow {
     prefixes_ch = channel.from('r1', 'r2', 'r3')
     constant_ch = channel.of(params.constant)
     inputs_ch   = prefixes_ch.combine(constant_ch)
     RNG(inputs_ch)
     RNG.output.values.view()
+    EXEC_FOO(inputs_ch)
 }

From 74babc73ee7b445343dfeab29e26830d7583088c Mon Sep 17 00:00:00 2001
From: Stephen Kelly <stevekm@users.noreply.github.com>
Date: Mon, 25 Mar 2024 12:31:59 -0400
Subject: [PATCH 2/2] update README dev instructions

---
 README.md | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index fcdd3ce..55b99f3 100644
--- a/README.md
+++ b/README.md
@@ -95,6 +95,17 @@ mv -f settings.gradle.bkp settings.gradle
 ./launch.sh run test.nf -plugins nf-prov
 ```
 
+An alternative method to build and test the plugin for development purposes;
+
+```bash
+# builds the plugin .zip and copies it to the local ${HOME}/.nextflow/plugins,
+# removing any pre-existing version
+make install
+
+# run with an externally installed nextflow using the included test workflow & config
+nextflow run tests/test.nf
+```
+
 ## Package, Upload, and Publish
 
 The project should hosted in a GitHub repository whose name should match the name of the plugin,
@@ -122,6 +133,6 @@ Following these step to package, upload and publish the plugin:
     ./gradlew :plugins:nf-prov:upload
     ```
 
-4. Create a pull request against the [nextflow-io/plugins](https://github.com/nextflow-io/plugins/blob/main/plugins.json) 
-  project to make the plugin public accessible to Nextflow app. 
+4. Create a pull request against the [nextflow-io/plugins](https://github.com/nextflow-io/plugins/blob/main/plugins.json)
+  project to make the plugin public accessible to Nextflow app.