Template update for nf-core/tools version 1.10.2

.github/CONTRIBUTING.md

@@ -46,7 +46,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Patch
 
-: warning: Only in the unlikely and regretful event of a release happening with a bug.
+:warning: Only in the unlikely and regretful event of a release happening with a bug.
 
 * On your own fork, make a new branch `patch` based on `upstream/master`.
 * Fix the bug, and bump version (X.Y.Z+1).

.github/workflows/awsfulltest.yml

@@ -21,7 +21,7 @@ jobs:
         run: conda install -c conda-forge awscli
       - name: Start AWS batch job
         # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples) 
+        # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
         env:

.github/workflows/branch.yml

@@ -17,6 +17,7 @@ jobs:
 
 
       # If the above check failed, post a comment on the PR explaining the failure
+      # 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

.github/workflows/linting.yml

@@ -57,5 +57,12 @@ jobs:
           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 lint ${GITHUB_WORKSPACE}
+        run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE}
+
+      - name: Upload linting log file artifact
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: linting-log-file
+          path: lint_log.txt
 

.github/workflows/push_dockerhub.yml

@@ -8,32 +8,33 @@ on:
   release:
     types: [published]
 
-push_dockerhub:
-  name: Push new Docker image to Docker Hub
-  runs-on: ubuntu-latest
-  # Only run for the nf-core repo, for releases and merged PRs
-  if: ${{ github.repository == 'nf-core/gwas' }}
-  env:
-    DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
-    DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
-  steps:
-    - name: Check out pipeline code
-      uses: actions/checkout@v2
+jobs:
+  push_dockerhub:
+    name: Push new Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    # Only run for the nf-core repo, for releases and merged PRs
+    if: ${{ github.repository == 'nf-core/gwas' }}
+    env:
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
 
-    - name: Build new docker image
-      run: docker build --no-cache . -t nfcore/gwas:latest
+      - name: Build new docker image
+        run: docker build --no-cache . -t nfcore/gwas:latest
 
-    - name: Push Docker image to DockerHub (dev)
-      if: ${{ github.event_name == 'push' }}
-      run: |
-        echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-        docker tag nfcore/gwas:latest nfcore/gwas:dev
-        docker push nfcore/gwas:dev
+      - name: Push Docker image to DockerHub (dev)
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker tag nfcore/gwas:latest nfcore/gwas:dev
+          docker push nfcore/gwas:dev
 
-    - name: Push Docker image to DockerHub (release)
-      if: ${{ github.event_name == 'release' }}
-      run: |
-        echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-        docker push nfcore/gwas:latest
-        docker tag nfcore/gwas:latest nfcore/gwas:${{ github.event.release.tag_name }}
-        docker push nfcore/gwas:${{ github.event.release.tag_name }}
+      - name: Push Docker image to DockerHub (release)
+        if: ${{ github.event_name == 'release' }}
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker push nfcore/gwas:latest
+          docker tag nfcore/gwas:latest nfcore/gwas:${{ github.event.release.tag_name }}
+          docker push nfcore/gwas:${{ github.event.release.tag_name }}

Dockerfile

@@ -1,4 +1,4 @@
-FROM nfcore/base:1.10.1
+FROM nfcore/base:1.10.2
 LABEL authors="Jesper Gådin" \
       description="Docker image containing all software requirements for the nf-core/gwas pipeline"