Basic configs and structure

Config according to sanger-tol pipelines doc 'create_pipeline'
Add subworkflow files
Implement two features VCFTOOLS_SITE_PI and VCFTOOLS_HET

Author: yz533cb

.github/workflows/branch.yml

@@ -1,17 +1,16 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to `main`/`master` branch on the repository
-# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
+# This workflow is triggered on PRs to `main` branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main` branch instead of `dev`
 on:
   pull_request_target:
     branches:
       - main
-      - master
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'sanger-tol/variantcomposition'
         run: |

.github/workflows/download_pipeline.yml

@@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core pipelines download'
 
 # Run the workflow when:
 #  - dispatched manually
-#  - when a PR is opened or reopened to main/master branch
+#  - when a PR is opened or reopened to main branch
 #  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
 on:
   workflow_dispatch:
@@ -14,7 +14,6 @@ on:
   pull_request:
     branches:
       - main
-      - master
 
 env:
   NXF_ANSI_LOG: false

.github/workflows/linting.yml

@@ -50,15 +50,15 @@ jobs:
           pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'master' }}
+        if: ${{ github.base_ref != 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Run nf-core pipelines lint --release
-        if: ${{ github.base_ref == 'master' }}
+        if: ${{ github.base_ref == 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/nf-test.yml

@@ -75,7 +75,7 @@ jobs:
         shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
         profile: [conda, docker, singularity]
         isMain:
-          - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
+          - ${{ github.base_ref == 'main' }}
         # Exclude conda and singularity on dev
         exclude:
           - isMain: false

modules.json

@@ -4,7 +4,13 @@
     "repos": {
         "https://github.com/nf-core/modules.git": {
             "modules": {
-                "nf-core": {}
+                "nf-core": {
+                    "vcftools": {
+                        "branch": "master",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "installed_by": ["modules"]
+                    }
+                }
             },
             "subworkflows": {
                 "nf-core": {