updated files to match editorconfig linting

.github/workflows/branch.yml

@@ -19,7 +19,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@v1
+        uses: mshick/add-pr-comment@v2
         with:
           message: |
             ## This PR is against the `master` branch :x:

.github/workflows/linting.yml

@@ -11,61 +11,22 @@ on:
     types: [published]
 
 jobs:
-  EditorConfig:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v4
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
-
-  Prettier:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-node@v4
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check ${GITHUB_WORKSPACE}
-
-  PythonBlack:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Check code lints with Black
-        uses: psf/black@stable
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          message: |
-            ## Python linting (`black`) is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
-            * Fix formatting errors in your pipeline: `black .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
+          python-version: 3.11
+          cache: "pip"
 
-            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+      - name: Run pre-commit
+        run: pre-commit run --all-files
 
   nf-core:
     runs-on: ubuntu-latest
@@ -76,7 +37,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
           architecture: "x64"
@@ -99,7 +60,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@v2
+        uses: dawidd6/action-download-artifact@v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.prettierrc

@@ -0,0 +1,4 @@
+{
+    "tabWidth": 4,
+    "useTabs": false
+}

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 
+Copyright (c)
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -44,9 +44,9 @@ Now, you can run the pipeline using:
 
 ```bash
 nextflow run nf-core/omicsgenetraitassociation \
-   -profile <docker/singularity/.../institute> \
-   --input samplesheet.csv \
-   --outdir <OUTDIR>
+  -profile <docker/singularity/.../institute> \
+  --input samplesheet.csv \
+  --outdir <OUTDIR>
 ```
 
 > [!WARNING]

assets/email_template.html

@@ -12,7 +12,7 @@
 
 <img src="cid:nfcorepipelinelogo">
 
-<h1>nf-core/omicsgenetraitassociation v${version}</h1>
+<h1>nf-core/omicsgenetraitassociation ${version}</h1>
 <h2>Run Name: $runName</h2>
 
 <% if (!success){

assets/email_template.txt

@@ -4,7 +4,7 @@
   |\\ | |__  __ /  ` /  \\ |__) |__         }  {
   | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
                                         `._,._,'
-  nf-core/omicsgenetraitassociation v${version}
+  nf-core/omicsgenetraitassociation ${version}
 ----------------------------------------------------
 Run Name: $runName
 

conf/cma_mea.config

@@ -37,9 +37,9 @@ process {
 
 
 singularity {
-  enabled = true
-  autoMounts = true
-  cacheDir = "singularity_images"
+    enabled = true
+    autoMounts = true
+    cacheDir = "singularity_images"
 }
 
 conda.enabled = true

conf/modules.config

@@ -19,79 +19,79 @@ process {
     ]
 
     withName: MMAP {
-      publishDir = [
-        path: { "${params.outdir}/mmap/mmap" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.endsWith('.poly.cov.csv') ? filename : null }
-      ]
+        publishDir = [
+            path: { "${params.outdir}/mmap/mmap" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.endsWith('.poly.cov.csv') ? filename : null }
+        ]
     }
 
     withName: MMAP_PARSE {
-      publishDir = [
-        path: { "${params.outdir}/mmap" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.startsWith('parsed_output_') ? filename : null }
-      ]
+        publishDir = [
+            path: { "${params.outdir}/mmap" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.startsWith('parsed_output_') ? filename : null }
+        ]
     }
 
     withName: PREPROCESS_PASCAL {
-      publishDir = [
-        path: { "${params.outdir}/mea" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename } 
-      ]
+        publishDir = [
+            path: { "${params.outdir}/mea" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
 
     withName: RUN_PASCAL {
-      publishDir = [
-        path: { "${params.outdir}/mea" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> 
-            if (filename.equals('versions.yml')) { null } 
-            else if (filename.startsWith('GO_')) { null }
-            else if (filename.startsWith('GS_')) { null }
-            else { filename } 
-        }
-      ]
+        publishDir = [
+            path: { "${params.outdir}/mea" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                if (filename.equals('versions.yml')) { null }
+                else if (filename.startsWith('GO_')) { null }
+                else if (filename.startsWith('GS_')) { null }
+                else { filename }
+            }
+        ]
     }
 
     withName: POSTPROCESS_PASCAL {
-      publishDir = [
-        path: { "${params.outdir}/mea" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> 
-            if (filename.equals('versions.yml')) { null } 
-            else if (filename.startsWith('GO_')) { null }
-            else if (filename.startsWith('GS_')) { null }
-            else { filename } 
-        }
-      ]
+        publishDir = [
+            path: { "${params.outdir}/mea" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                if (filename.equals('versions.yml')) { null }
+                else if (filename.startsWith('GO_')) { null }
+                else if (filename.startsWith('GS_')) { null }
+                else { filename }
+            }
+        ]
     }
 
     withName: GO_ANALYSIS {
-      publishDir = [
-        path: { "${params.outdir}/mea/" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> 
-            if (filename.equals('versions.yml')) { null } 
-            else if (filename.endsWith(".txt")) { null }
-            else if (filename.startsWith('GS_')) { null }
-            else { filename } 
+        publishDir = [
+            path: { "${params.outdir}/mea/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                if (filename.equals('versions.yml')) { null }
+                else if (filename.endsWith(".txt")) { null }
+                else if (filename.startsWith('GS_')) { null }
+                else { filename }
+            }
+        ]
         }
-      ]
-    }
 
     withName: MERGE_ORA_AND_SUMMARY {
-      publishDir = [
-        path: { "${params.outdir}/mea/" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> 
-            if (filename.equals('versions.yml')) { null } 
-            else if (filename.startsWith('GO_')) { null }
-            else if (filename.startsWith('GS_')) { null }
-            else { filename } 
-        }
-      ]
+        publishDir = [
+            path: { "${params.outdir}/mea/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                if (filename.equals('versions.yml')) { null }
+                else if (filename.startsWith('GO_')) { null }
+                else if (filename.startsWith('GS_')) { null }
+                else { filename }
+            }
+        ]
     }
 
     withName: SAMPLESHEET_CHECK {
@@ -101,25 +101,4 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-
-    //withName: FASTQC {
-    //    ext.args = '--quiet'
-    //}
-
-    //withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-    //    publishDir = [
-    //        path: { "${params.outdir}/pipeline_info" },
-    //        mode: params.publish_dir_mode,
-    //        pattern: '*_versions.yml'
-    //    ]
-    //}
-
-    //withName: 'MULTIQC' {
-    //    ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
-    //    publishDir = [
-    //        path: { "${params.outdir}/multiqc" },
-    //        mode: params.publish_dir_mode,
-    //        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    //    ]
-    //}
 }