From 17390746ea2cc6edf8dcb306a5c24473a01e2db0 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 11 Aug 2023 16:33:19 +0000
Subject: [PATCH 01/22] Add automated linting fixer workflow

---
 .devcontainer/devcontainer.json   | 11 +++----
 .github/workflows/fix-linting.yml | 48 +++++++++++++++++++++++++++++++
 2 files changed, 54 insertions(+), 5 deletions(-)
 create mode 100644 .github/workflows/fix-linting.yml

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index bf55f53..fa08225 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -4,11 +4,12 @@
   "customizations": {
     "vscode": {
       "extensions": [
-        "nextflow.nextflow",
-        "esbenp.prettier-vscode",
-        "redhat.vscode-yaml",
-        "GitHub.vscode-pull-request-github"
-      ]
+		"nextflow.nextflow",
+		"esbenp.prettier-vscode",
+		"redhat.vscode-yaml",
+		"GitHub.vscode-pull-request-github",
+		"github.vscode-github-actions"
+	]
     }
   }
 }
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
new file mode 100644
index 0000000..3763637
--- /dev/null
+++ b/.github/workflows/fix-linting.yml
@@ -0,0 +1,48 @@
+name: Fix linting from a comment
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  deploy:
+    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
+    if: >
+      contains(github.event.comment.html_url, '/pull/') &&
+      contains(github.event.comment.body, 'fix-linting') &&
+      github.repository == 'adamrtalbot/nf-canary'
+    runs-on: ubuntu-latest
+    steps:
+      # Use the @nf-core-bot token to check out so we can push later
+      - uses: actions/checkout@v3
+
+      # Action runs on the issue comment, so we don't get the PR by default
+      # Use the gh cli to check out the PR
+      - name: Checkout Pull Request
+        run: gh pr checkout ${{ github.event.issue.number }}
+
+      - uses: actions/setup-node@v3
+
+      - name: Install Prettier
+        run: npm install -g prettier @prettier/plugin-php
+
+      # Check that we actually need to fix something
+      - name: Run 'prettier --check'
+        id: prettier_status
+        run: |
+          if prettier --check ${GITHUB_WORKSPACE}; then
+            echo "result=pass" >> $GITHUB_OUTPUT
+          else
+            echo "result=fail" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Run 'prettier --write'
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: prettier --write ${GITHUB_WORKSPACE}
+
+      - name: Commit & push changes
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: |
+          git config --global user.name 'adamrtalbot'
+          git config --global user.email 'adamrtalbot@users.noreply.github.com'
+          git commit -am "[automated] Fix linting with Prettier"
+          git push
\ No newline at end of file

From 60b112cc8562c372fe56fa5e694c119700b80a3b Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 08:50:27 +0000
Subject: [PATCH 02/22] fix linting

---
 .devcontainer/devcontainer.json   | 12 ++++++------
 .github/workflows/fix-linting.yml |  4 ++--
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index fa08225..c185419 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -4,12 +4,12 @@
   "customizations": {
     "vscode": {
       "extensions": [
-		"nextflow.nextflow",
-		"esbenp.prettier-vscode",
-		"redhat.vscode-yaml",
-		"GitHub.vscode-pull-request-github",
-		"github.vscode-github-actions"
-	]
+        "nextflow.nextflow",
+        "esbenp.prettier-vscode",
+        "redhat.vscode-yaml",
+        "GitHub.vscode-pull-request-github",
+        "github.vscode-github-actions"
+      ]
     }
   }
 }
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 3763637..eebcf9d 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -4,7 +4,7 @@ on:
     types: [created]
 
 jobs:
-  deploy:
+  fix:
     # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
@@ -45,4 +45,4 @@ jobs:
           git config --global user.name 'adamrtalbot'
           git config --global user.email 'adamrtalbot@users.noreply.github.com'
           git commit -am "[automated] Fix linting with Prettier"
-          git push
\ No newline at end of file
+          git push

From 58ae3fa21c181051b23513bd0ae75226f6cf6bac Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 09:06:30 +0000
Subject: [PATCH 03/22] Added automatic linting to Github action with prettier

---
 .github/workflows/fix-linting.yml           | 48 ---------------------
 .github/workflows/{nf-test.yml => test.yml} |  4 ++
 2 files changed, 4 insertions(+), 48 deletions(-)
 delete mode 100644 .github/workflows/fix-linting.yml
 rename .github/workflows/{nf-test.yml => test.yml} (95%)

diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
deleted file mode 100644
index eebcf9d..0000000
--- a/.github/workflows/fix-linting.yml
+++ /dev/null
@@ -1,48 +0,0 @@
-name: Fix linting from a comment
-on:
-  issue_comment:
-    types: [created]
-
-jobs:
-  fix:
-    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
-    if: >
-      contains(github.event.comment.html_url, '/pull/') &&
-      contains(github.event.comment.body, 'fix-linting') &&
-      github.repository == 'adamrtalbot/nf-canary'
-    runs-on: ubuntu-latest
-    steps:
-      # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
-
-      # Action runs on the issue comment, so we don't get the PR by default
-      # Use the gh cli to check out the PR
-      - name: Checkout Pull Request
-        run: gh pr checkout ${{ github.event.issue.number }}
-
-      - uses: actions/setup-node@v3
-
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
-
-      # Check that we actually need to fix something
-      - name: Run 'prettier --check'
-        id: prettier_status
-        run: |
-          if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "result=pass" >> $GITHUB_OUTPUT
-          else
-            echo "result=fail" >> $GITHUB_OUTPUT
-          fi
-
-      - name: Run 'prettier --write'
-        if: steps.prettier_status.outputs.result == 'fail'
-        run: prettier --write ${GITHUB_WORKSPACE}
-
-      - name: Commit & push changes
-        if: steps.prettier_status.outputs.result == 'fail'
-        run: |
-          git config --global user.name 'adamrtalbot'
-          git config --global user.email 'adamrtalbot@users.noreply.github.com'
-          git commit -am "[automated] Fix linting with Prettier"
-          git push
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/test.yml
similarity index 95%
rename from .github/workflows/nf-test.yml
rename to .github/workflows/test.yml
index ba823c0..7ecdb63 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/test.yml
@@ -30,11 +30,15 @@ jobs:
       - name: Install Prettier
         run: npm install -g prettier
 
+      - name: Prettier Action
+        uses: creyD/prettier_action@v4.3
+
       - name: Run Prettier --check
         run: prettier --check .
 
   nf-test:
     runs-on: ubuntu-20.04
+    needs: prettier
     env:
       NXF_ANSI_LOG: false
     steps:

From 966b60d42fbb9a30c5d68b00af21eec472f9dae2 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 09:08:58 +0000
Subject: [PATCH 04/22] messed up workflow

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 7ecdb63..5d82c60 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -18,7 +18,7 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  prettier:
+  prettier:   
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository

From 489fe3404672407790363f31cb3055479095b1b2 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 09:10:21 +0000
Subject: [PATCH 05/22] more messing up

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 5d82c60..dbc31d1 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -18,7 +18,7 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  prettier:   
+  prettier:     
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository

From d65121505ee7bdaa994922f3b2aa64dd8eb09b3b Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 09:12:52 +0000
Subject: [PATCH 06/22] Added path to prettier

---
 .github/workflows/test.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index dbc31d1..378f3b6 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -32,6 +32,9 @@ jobs:
 
       - name: Prettier Action
         uses: creyD/prettier_action@v4.3
+        prettier_options: 
+          - "--write"
+          - "**/*"
 
       - name: Run Prettier --check
         run: prettier --check .

From 23674333a55d7b75a3ba29b23209b257d745f864 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 09:21:06 +0000
Subject: [PATCH 07/22] Update prettier

---
 .editorconfig              | 12 ++++++++++++
 .github/workflows/test.yml |  6 +++---
 .prettierignore            | 14 ++++++++++----
 3 files changed, 25 insertions(+), 7 deletions(-)
 create mode 100644 .editorconfig

diff --git a/.editorconfig b/.editorconfig
new file mode 100644
index 0000000..16576f3
--- /dev/null
+++ b/.editorconfig
@@ -0,0 +1,12 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{md,yml,yaml,cff}]
+indent_size = 2
\ No newline at end of file
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 378f3b6..b6ce5c6 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -18,7 +18,7 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  prettier:     
+  prettier:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
@@ -32,9 +32,9 @@ jobs:
 
       - name: Prettier Action
         uses: creyD/prettier_action@v4.3
-        prettier_options: 
+        prettier_options:
           - "--write"
-          - "**/*"
+          - "'*'"
 
       - name: Run Prettier --check
         run: prettier --check .
diff --git a/.prettierignore b/.prettierignore
index 676bcd1..5d66077 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,9 +1,15 @@
 .nextflow*
+.editorconfig
+.gitignore
+.prettierignore
+LICENSE
 work/
-data/
 results/
 .DS_Store
-testing/
-testing*
 *.pyc
-bin/
+*.nf
+*.config
+*.test
+*.test.snap
+*.txt
+

From b04925408f2dd43b56afa0d141e8f311ffc621f4 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 09:21:58 +0000
Subject: [PATCH 08/22] Fix workflow

---
 .github/workflows/test.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index b6ce5c6..d6d2fd9 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -32,9 +32,10 @@ jobs:
 
       - name: Prettier Action
         uses: creyD/prettier_action@v4.3
-        prettier_options:
-          - "--write"
-          - "'*'"
+        with:
+          prettier_options:
+            - "--write"
+            - "'*'"
 
       - name: Run Prettier --check
         run: prettier --check .

From 1ea62ba0ab892932c23147395196954c20e07326 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 09:22:51 +0000
Subject: [PATCH 09/22] fix

---
 .github/workflows/test.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index d6d2fd9..193e427 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -33,9 +33,7 @@ jobs:
       - name: Prettier Action
         uses: creyD/prettier_action@v4.3
         with:
-          prettier_options:
-            - "--write"
-            - "'*'"
+          prettier_options: "--write '*'"
 
       - name: Run Prettier --check
         run: prettier --check .

From 88f966c46a839e9b32bd005efae5a408fad0e466 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 09:30:05 +0000
Subject: [PATCH 10/22] fixy

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 193e427..fa5d180 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -33,7 +33,7 @@ jobs:
       - name: Prettier Action
         uses: creyD/prettier_action@v4.3
         with:
-          prettier_options: "--write '*'"
+          prettier_options: '--write "*"'
 
       - name: Run Prettier --check
         run: prettier --check .

From 3f12b47851d8e8f73355e3fd7a72da97e424c41d Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 09:32:17 +0000
Subject: [PATCH 11/22] fixy 2

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index fa5d180..3ac4a9a 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -33,7 +33,7 @@ jobs:
       - name: Prettier Action
         uses: creyD/prettier_action@v4.3
         with:
-          prettier_options: '--write "*"'
+          prettier_options: '--write *'
 
       - name: Run Prettier --check
         run: prettier --check .

From cf4e9e90ca36b9bd8daed7b43f629a20f1fedd9e Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 09:36:14 +0000
Subject: [PATCH 12/22] fixy 3

---
 .devcontainer/devcontainer.json |  2 +-
 .github/workflows/test.yml      |  2 +-
 nextflow_schema.json            | 69 ++++++++++++++++-----------------
 3 files changed, 36 insertions(+), 37 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index c185419..ed16369 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -7,7 +7,7 @@
         "nextflow.nextflow",
         "esbenp.prettier-vscode",
         "redhat.vscode-yaml",
-        "GitHub.vscode-pull-request-github",
+        "GitHub.vscode-pull-request-github", 
         "github.vscode-github-actions"
       ]
     }
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 3ac4a9a..193e427 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -33,7 +33,7 @@ jobs:
       - name: Prettier Action
         uses: creyD/prettier_action@v4.3
         with:
-          prettier_options: '--write *'
+          prettier_options: "--write '*'"
 
       - name: Run Prettier --check
         run: prettier --check .
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 8a90bb9..d50c112 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,38 +1,37 @@
 {
-  "$schema": "http://json-schema.org/draft-07/schema",
-  "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
-  "title": ". pipeline parameters",
-  "description": "",
-  "type": "object",
-  "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."
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
+    "title": ". pipeline parameters",
+    "description": "",
+    "type": "object",
+    "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": [
-    {
-      "$ref": "#/definitions/parameters"
-    }
-  ]
+    },
+    "allOf": [
+        {
+            "$ref": "#/definitions/parameters"
+        }
+    ]
 }

From 91960abc51e64dd94f19081738011b4168a7c81a Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 09:36:59 +0000
Subject: [PATCH 13/22] fixy 4

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 193e427..b17f439 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -33,7 +33,7 @@ jobs:
       - name: Prettier Action
         uses: creyD/prettier_action@v4.3
         with:
-          prettier_options: "--write '*'"
+          prettier_options: "--write '**/*'"
 
       - name: Run Prettier --check
         run: prettier --check .

From de942039bf92b45730739f770924d0e3cad80d36 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 09:42:27 +0000
Subject: [PATCH 14/22] FIxy 5

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index b17f439..a466b32 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -33,7 +33,7 @@ jobs:
       - name: Prettier Action
         uses: creyD/prettier_action@v4.3
         with:
-          prettier_options: "--write '**/*'"
+          prettier_options: '--write "./**/*"'
 
       - name: Run Prettier --check
         run: prettier --check .

From e830bf9c3060b2331abbc247da9407f0b816b3d1 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 09:57:02 +0000
Subject: [PATCH 15/22] Explicit file pattern fixes

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a466b32..411818b 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -33,7 +33,7 @@ jobs:
       - name: Prettier Action
         uses: creyD/prettier_action@v4.3
         with:
-          prettier_options: '--write "./**/*"'
+          prettier_options: '--write **/*.{json,yaml,yml,sh,md}'
 
       - name: Run Prettier --check
         run: prettier --check .

From 7921a2c19da8526d0eddad2c97ae3967dd22ed4f Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 09:59:55 +0000
Subject: [PATCH 16/22] fixy 6

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 411818b..065e993 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -33,7 +33,7 @@ jobs:
       - name: Prettier Action
         uses: creyD/prettier_action@v4.3
         with:
-          prettier_options: '--write **/*.{json,yaml,yml,sh,md}'
+          prettier_options: '--write **/*.{json,yaml,yml,md}'
 
       - name: Run Prettier --check
         run: prettier --check .

From 348888876ef2d8ea133b9e24dd9bf4da8b3b9af8 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 10:02:50 +0000
Subject: [PATCH 17/22] fixy 7

---
 .github/workflows/test.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 065e993..219723a 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -23,6 +23,9 @@ jobs:
     steps:
       - name: Check out repository
         uses: actions/checkout@v3
+        with:
+          ref: ${{ github.head_ref }}
+          fetch-depth: 0
 
       - name: Install NodeJS
         uses: actions/setup-node@v3
@@ -34,6 +37,7 @@ jobs:
         uses: creyD/prettier_action@v4.3
         with:
           prettier_options: '--write **/*.{json,yaml,yml,md}'
+          only_changed: True
 
       - name: Run Prettier --check
         run: prettier --check .

From 43b641eb282311c2c8d4341feaa42250b8506fad Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 10:06:19 +0000
Subject: [PATCH 18/22] Add write permissions

---
 .github/workflows/test.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 219723a..82b1fc0 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -17,6 +17,9 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+permissions:
+  contents: write
+
 jobs:
   prettier:
     runs-on: ubuntu-latest

From 08af8209b218a3ad995530552de64fb76b0ee4c6 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 10:08:10 +0000
Subject: [PATCH 19/22] update permissions

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 82b1fc0..acfce29 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -18,6 +18,7 @@ concurrency:
   cancel-in-progress: true
 
 permissions:
+  actions: write
   contents: write
 
 jobs:

From cc5ccd89c2e3dae0a6799e71079d4e4e454f6fb1 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 10:11:16 +0000
Subject: [PATCH 20/22] stuff

---
 .devcontainer/devcontainer.json | 24 ++++++++++++------------
 .github/workflows/test.yml      |  7 -------
 .prettierignore                 |  1 +
 nextflow_schema.json            |  3 ++-
 4 files changed, 15 insertions(+), 20 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index ed16369..13a7bed 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,15 +1,15 @@
 {
-  "image": "docker.io/nfcore/gitpod:2.9",
-  "features": {},
-  "customizations": {
-    "vscode": {
-      "extensions": [
-        "nextflow.nextflow",
-        "esbenp.prettier-vscode",
-        "redhat.vscode-yaml",
-        "GitHub.vscode-pull-request-github", 
-        "github.vscode-github-actions"
-      ]
+    "image": "docker.io/nfcore/gitpod:2.9",
+    "features": {},
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "nextflow.nextflow",
+                "esbenp.prettier-vscode",
+                "redhat.vscode-yaml",
+                "GitHub.vscode-pull-request-github",
+                "github.vscode-github-actions"
+            ]
+        }
     }
-  }
 }
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index acfce29..8afb8d7 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -18,7 +18,6 @@ concurrency:
   cancel-in-progress: true
 
 permissions:
-  actions: write
   contents: write
 
 jobs:
@@ -37,12 +36,6 @@ jobs:
       - name: Install Prettier
         run: npm install -g prettier
 
-      - name: Prettier Action
-        uses: creyD/prettier_action@v4.3
-        with:
-          prettier_options: '--write **/*.{json,yaml,yml,md}'
-          only_changed: True
-
       - name: Run Prettier --check
         run: prettier --check .
 
diff --git a/.prettierignore b/.prettierignore
index 5d66077..94f5706 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -6,6 +6,7 @@ LICENSE
 work/
 results/
 .DS_Store
+*.sh
 *.pyc
 *.nf
 *.config
diff --git a/nextflow_schema.json b/nextflow_schema.json
index d50c112..387b6b6 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -11,7 +11,8 @@
             "description": "",
             "default": "",
             "properties": {
-                "skip": { "type": "string",
+                "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."
                 },

From 240164da24b1e10fa04192fa09c917bfe1da86a0 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 10:11:45 +0000
Subject: [PATCH 21/22] Remove dependency

---
 .github/workflows/test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 8afb8d7..989cc99 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -41,7 +41,6 @@ jobs:
 
   nf-test:
     runs-on: ubuntu-20.04
-    needs: prettier
     env:
       NXF_ANSI_LOG: false
     steps:

From 5172bcab7aac6326fe6850db81b25d8e2be0152f Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 15 Aug 2023 16:20:14 +0000
Subject: [PATCH 22/22] Revert test.yml

---
 .github/workflows/test.yml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 989cc99..ba823c0 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -17,18 +17,12 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
-permissions:
-  contents: write
-
 jobs:
   prettier:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
         uses: actions/checkout@v3
-        with:
-          ref: ${{ github.head_ref }}
-          fetch-depth: 0
 
       - name: Install NodeJS
         uses: actions/setup-node@v3