Template update for nf-core/tools version 1.13

.github/.dockstore.yml

@@ -3,3 +3,4 @@ version: 1.2
 workflows:
   - subclass: nfl
     primaryDescriptorPath: /nextflow.config
+    publish: True

.github/CONTRIBUTING.md

@@ -87,7 +87,7 @@ Once there, use `nf-core schema build .` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
 

.github/ISSUE_TEMPLATE/bug_report.md

@@ -55,7 +55,7 @@ Have you provided the following extra information/files:
 
 ## Container engine
 
-- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
+- Engine: <!-- [e.g. Conda, Docker, Singularity, Podman, Shifter or Charliecloud] -->
 - version: <!-- [e.g. 1.0.0] -->
 - Image tag: <!-- [e.g. nfcore/cutandrun:1.0.0] -->
 

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,6 +1,6 @@
 ---
 name: Feature request
-about: Suggest an idea for the nf-core website
+about: Suggest an idea for the nf-core/cutandrun pipeline
 labels: enhancement
 ---
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,9 +15,9 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/cuta
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
- - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
- - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/cutandrun/tree/master/.github/CONTRIBUTING.md)
- - [ ] If necessary, also make a PR on the nf-core/cutandrun _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+  - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
+  - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/cutandrun/tree/master/.github/CONTRIBUTING.md)
+  - [ ] If necessary, also make a PR on the nf-core/cutandrun _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint .`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/awsfulltest.yml

@@ -9,6 +9,16 @@ on:
     types: [completed]
   workflow_dispatch:
 
+
+env:
+  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+  TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
+  AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
+  AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
+  AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
+
+
 jobs:
   run-awstest:
     name: Run AWS full tests
@@ -27,13 +37,6 @@ jobs:
         # 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:
-          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
-          AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
-          AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
-          AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
         run: |
           aws batch submit-job \
             --region eu-west-1 \

.github/workflows/awstest.yml

@@ -6,6 +6,16 @@ name: nf-core AWS test
 on:
   workflow_dispatch:
 
+
+env:
+  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+  TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
+  AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
+  AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
+  AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
+
+
 jobs:
   run-awstest:
     name: Run AWS tests
@@ -23,13 +33,6 @@ jobs:
         # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
-        env:
-          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
-          AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
-          AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
-          AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
         run: |
           aws batch submit-job \
           --region eu-west-1 \

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/cutandrun'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/cutandrun ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/cutandrun ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
 
       # If the above check failed, post a comment on the PR explaining the failure
@@ -25,11 +25,12 @@ jobs:
           message: |
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
+            It looks like this pull-request is has been made against the ${{github.event.pull_request.base.repo.full_name }} `master` branch.
             The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
+            Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.base.repo.full_name }} `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
+            Note that even after this, the test will continue to show as failing until you push a new commit.
 
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/ci.yml

@@ -20,11 +20,28 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: [20.11.0-edge]
+        nxf_ver: ['20.04.0', '']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - name: Check if Dockerfile or Conda environment changed
+        uses: technote-space/get-diff-action@v4
+        with:
+          FILES: |
+            Dockerfile
+            environment.yml
+
+      - name: Build new docker image
+        if: env.MATCHED_FILES
+        run: docker build --no-cache . -t nfcore/cutandrun:dev
+
+      - name: Pull docker image
+        if: ${{ !env.MATCHED_FILES }}
+        run: |
+          docker pull nfcore/cutandrun:dev
+          docker tag nfcore/cutandrun:dev nfcore/cutandrun:dev
+
       - name: Install Nextflow
         env:
           CAPSULE_LOG: none

.github/workflows/linting.yml

@@ -69,7 +69,7 @@ jobs:
         if: ${{ always() }}
         uses: actions/upload-artifact@v2
         with:
-          name: linting-log-file
+          name: linting-logs
           path: |
             lint_log.txt
             lint_results.md

.github/workflows/push_dockerhub_dev.yml

@@ -0,0 +1,28 @@
+name: nf-core Docker push (dev)
+# This builds the docker image and pushes it to DockerHub
+# Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
+on:
+  push:
+    branches:
+      - dev
+
+jobs:
+  push_dockerhub:
+    name: Push new Docker image to Docker Hub (dev)
+    runs-on: ubuntu-latest
+    # Only run for the nf-core repo, for releases and merged PRs
+    if: ${{ github.repository == 'nf-core/cutandrun' }}
+    env:
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Build new docker image
+        run: docker build --no-cache . -t nfcore/cutandrun:dev
+
+      - name: Push Docker image to DockerHub (dev)
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker push nfcore/cutandrun:dev

.github/workflows/push_dockerhub_release.yml

@@ -0,0 +1,29 @@
+name: nf-core Docker push (release)
+# This builds the docker image and pushes it to DockerHub
+# Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
+on:
+  release:
+    types: [published]
+
+jobs:
+  push_dockerhub:
+    name: Push new Docker image to Docker Hub (release)
+    runs-on: ubuntu-latest
+    # Only run for the nf-core repo, for releases and merged PRs
+    if: ${{ github.repository == 'nf-core/cutandrun' }}
+    env:
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Build new docker image
+        run: docker build --no-cache . -t nfcore/cutandrun:latest
+
+      - name: Push Docker image to DockerHub (release)
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker push nfcore/cutandrun:latest
+          docker tag nfcore/cutandrun:latest nfcore/cutandrun:${{ github.event.release.tag_name }}
+          docker push nfcore/cutandrun:${{ github.event.release.tag_name }}

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [1.0dev] - [date]
+## v1.0dev - [date]
 
 Initial release of nf-core/cutandrun, created with the [nf-core](https://nf-co.re/) template.