From cab334fcf5ed2649e4295d19b3ba963969138259 Mon Sep 17 00:00:00 2001
From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 19 May 2025 11:58:50 +0100
Subject: [PATCH 1/2] feat: New output syntax

---
 main.nf         | 24 +++++++++++++++++-------
 nextflow.config | 19 ++++++++++---------
 2 files changed, 27 insertions(+), 16 deletions(-)

diff --git a/main.nf b/main.nf
index a2c7484..c45c6f9 100644
--- a/main.nf
+++ b/main.nf
@@ -1,3 +1,5 @@
+nextflow.preview.output = true
+
 process TEST_SUCCESS {
     /*
     This process should automatically succeed
@@ -143,9 +145,6 @@ process TEST_PUBLISH_FILE {
     Creates a file on the worker node and uploads to the publish directory.
     */
 
-
-    publishDir { params.outdir ?: file(workflow.workDir).resolve("outputs").toUriString()  }, mode: 'copy'
-
     output:
         path("*.txt")
 
@@ -160,8 +159,6 @@ process TEST_PUBLISH_FOLDER {
     Creates a file on the worker node and uploads to the publish directory.
     */
 
-    publishDir { params.outdir ?: file(workflow.workDir).resolve("outputs").toUriString()  }, mode: 'copy'
-
     output:
         path("test", type: 'dir')
 
@@ -362,7 +359,7 @@ workflow NF_CANARY {
         TEST_MV_FILE()
         TEST_MV_FOLDER_CONTENTS()
         TEST_VAL_INPUT("Hello World")
-        
+
         TEST_GPU( dummy.filter { params.gpu } )
         // POC of emitting the channel
         Channel.empty()
@@ -390,5 +387,18 @@ workflow NF_CANARY {
 }
 
 workflow {
-    NF_CANARY()
+    main:
+    NF_CANARY().collect()
+
+    publish:
+    outputs = NF_CANARY.out.collect()
 }
+
+output {
+    outputs {
+        path "."
+        index {
+            path params.output_index
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 8edb0c6..db5f012 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,17 +1,18 @@
 params {
-    skip       = ''
-    gpu        = false
-    run        = null
-    outdir     = null
-    remoteFile = null
-    container  = "quay.io/biocontainers/ubuntu:24.04"
+    skip         = ''
+    gpu          = false
+    run          = null
+    outdir       = null
+    remoteFile   = null
+    output_index = "outputs.json"
+    container    = "quay.io/biocontainers/ubuntu:24.04"
 }
 
 process {
     container     = params.container
     errorStrategy = "finish"
-    when          = { 
-        ( params.run ? params.run.split(',').any{ "NF_CANARY:${it.toUpperCase()}".contains(task.process) } : true ) && 
-        (!params.skip.split(',').any{ "NF_CANARY:${it.toUpperCase()}".contains(task.process) } ) 
+    when          = {
+        ( params.run ? params.run.split(',').any{ "NF_CANARY:${it.toUpperCase()}".contains(task.process) } : true ) &&
+        (!params.skip.split(',').any{ "NF_CANARY:${it.toUpperCase()}".contains(task.process) } )
     }
 }

From 4f4e05ca6ea0281ec7befd69cf5188cf66c37ee1 Mon Sep 17 00:00:00 2001
From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Mon, 19 May 2025 11:59:13 +0100
Subject: [PATCH 2/2] Re-add old publishDir syntax back for continuity

---
 main.nf | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/main.nf b/main.nf
index c45c6f9..ebb7974 100644
--- a/main.nf
+++ b/main.nf
@@ -145,6 +145,9 @@ process TEST_PUBLISH_FILE {
     Creates a file on the worker node and uploads to the publish directory.
     */
 
+
+    publishDir { params.outdir ?: file(workflow.workDir).resolve("outputs").toUriString()  }, mode: 'copy'
+
     output:
         path("*.txt")
 
@@ -159,6 +162,8 @@ process TEST_PUBLISH_FOLDER {
     Creates a file on the worker node and uploads to the publish directory.
     */
 
+    publishDir { params.outdir ?: file(workflow.workDir).resolve("outputs").toUriString()  }, mode: 'copy'
+
     output:
         path("test", type: 'dir')