From a0e4f1704daba58069d0f74f8fe50b47ab842cb0 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Thu, 10 Aug 2023 11:05:28 +0100
Subject: [PATCH 1/3] Update docs to include parameter --outdir

---
 README.md            |  6 +++++-
 nextflow_schema.json | 42 ++++++++++++++++++++++++++++++------------
 2 files changed, 35 insertions(+), 13 deletions(-)

diff --git a/README.md b/README.md
index 4941ff5..c4e7eaa 100644
--- a/README.md
+++ b/README.md
@@ -91,7 +91,11 @@ This process stages a folder from the working directory to the worker node, copi
 
 ### `TEST_PUBLISH_FILE`
 
-This process creates a file on the worker machine, then writes that file to the publishDir directory. This is the by default written to an subfolder called `output` in the working directory.
+This process creates a file on the worker machine, then writes that file to the publishDir directory. This is the by default written to an subfolder called `output` in the working directory, but this can be overridden using the parameter `outdir`. Use this to demonstrate you are able to publish to the relevant output directory.
+
+### `TEST_PUBLISH_FOLDER`
+
+This process creates a folder on the worker machine, then writes that folder to the publishDir directory. This is the by default written to an subfolder called `output` in the working directory, but this can be overridden using the parameter `outdir`. Use this to demonstrate you are able to publish to the relevant output directory.
 
 ### `TEST_IGNORED_FAIL`
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 9b64ff4..8a90bb9 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -4,17 +4,35 @@
   "title": ". pipeline parameters",
   "description": "",
   "type": "object",
-  "properties": {
-    "skip": {
-      "type": "string",
-      "description": "Tests to skip as comma delimited values.",
-      "help_text": "Tests to skip as comma delimited values. E.g. --skip TEST_SUCCESS,TEST_INPUT. Case insensitive."
-    },
-    "remoteFile": {
-      "type": "string",
-      "description": "Path to remote file to download and use.",
-      "help_text": "Path to a remote file to use within the pipeline. This mimics a remote set of files such as reference data that may need to be retrieved prior to analysis. By default this is not specified and the test is not ran, add a remote file using standard Nextflow filenaming to pull a file from your storage (e.g. an S3 bucket or shared storage).",
-      "format": "path"
+  "definitions": {
+    "parameters": {
+      "title": "Parameters",
+      "type": "object",
+      "description": "",
+      "default": "",
+      "properties": {
+        "skip": {
+          "type": "string",
+          "description": "Tests to skip as comma delimited values.",
+          "help_text": "Tests to skip as comma delimited values. E.g. --skip TEST_SUCCESS,TEST_INPUT. Case insensitive."
+        },
+        "remoteFile": {
+          "type": "string",
+          "description": "Path to remote file to download and use.",
+          "help_text": "Path to a remote file to use within the pipeline. This mimics a remote set of files such as reference data that may need to be retrieved prior to analysis. By default this is not specified and the test is not ran, add a remote file using standard Nextflow filenaming to pull a file from your storage (e.g. an S3 bucket or shared storage).",
+          "format": "path"
+        },
+        "outdir": {
+          "type": "string",
+          "description": "Path to use for publishing output files.",
+          "help_text": "Path to a remote folder to publish files to. If not specified, this is a subfolder within the working directory but if specified it will publish files to the path specified in this parameter."
+        }
+      }
     }
-  }
+  },
+  "allOf": [
+    {
+      "$ref": "#/definitions/parameters"
+    }
+  ]
 }

From 55d397820f25cc0f6277be23d2b3b54d8f1e3774 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Thu, 10 Aug 2023 11:06:47 +0100
Subject: [PATCH 2/3] Change testing name to 'test' since it lints and tests

---
 .github/workflows/nf-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 756cc42..f96a360 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -1,4 +1,4 @@
-name: nf-test
+name: test
 on:
   push:
     branches: [main]

From 72afda3ad7026736c8db0ba19e82594684f6b660 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Thu, 10 Aug 2023 11:08:35 +0100
Subject: [PATCH 3/3] Update concurrency settings for GHA

---
 .github/workflows/nf-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index f96a360..ba823c0 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -14,7 +14,7 @@ on:
 
 # Cancel if a newer run is started
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 jobs: