Template update for nf-core/tools version 1.12

nf-core-bot · nf-core-bot · commit 82a71c94b148 · 2020-11-19T13:47:46.000Z
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -1,10 +1,15 @@
+---
+name: Bug report
+about: Report something that is broken or incorrect
+labels: bug
+---
+
 <!--
 # nf-core/rnaseq bug report
 
 Hi there!
 
 Thanks for telling us about a problem with the pipeline.
-
 Please delete this text and anything that's not relevant from the template below:
 -->
 
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: "Slack #rnaseq channel"
+    url: https://nfcore.slack.com/channels/rnaseq
+    about: Discussion about the nf-core/rnaseq pipeline
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -1,3 +1,9 @@
+---
+name: Feature request
+about: Suggest an idea for the nf-core website
+labels: enhancement
+---
+
 <!--
 # nf-core/rnaseq feature request
 
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -4,8 +4,9 @@ name: nf-core AWS full size tests
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
+  workflow_run:
+    workflows: ["nf-core Docker push (release)"]
+    types: [completed]
   workflow_dispatch:
 
 jobs:
@@ -15,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.0.2
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: 3.7
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.0.2
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: 3.7
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -2,7 +2,7 @@ name: nf-core branch protection
 # This workflow is triggered on PRs to master branch on the repository
 # It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
 on:
-  pull_request:
+  pull_request_target:
     branches: [master]
 
 jobs:
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -20,29 +20,31 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['19.10.0', '']
+        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@v1
+        uses: technote-space/get-diff-action@v4
         with:
-          PREFIX_FILTER: |
+          FILES: |
             Dockerfile
             environment.yml
 
       - name: Build new docker image
-        if: env.GIT_DIFF
+        if: env.MATCHED_FILES
         run: docker build --no-cache . -t nfcore/rnaseq:dev
 
       - name: Pull docker image
-        if: ${{ !env.GIT_DIFF }}
+        if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/rnaseq:dev
           docker tag nfcore/rnaseq:dev nfcore/rnaseq:dev
 
       - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -38,6 +38,8 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
@@ -57,12 +59,19 @@ 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 -l lint_log.txt lint ${GITHUB_WORKSPACE}
+        run: nf-core -l lint_log.txt lint ${GITHUB_WORKSPACE} --markdown lint_results.md
+
+      - name: Save PR number
+        if: ${{ always() }}
+        run: echo ${{ github.event.pull_request.number }} > PR_number.txt
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
         uses: actions/upload-artifact@v2
         with:
           name: linting-log-file
-          path: lint_log.txt
+          path: |
+            lint_log.txt
+            lint_results.md
+            PR_number.txt
 
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
@@ -0,0 +1,29 @@
+
+name: nf-core linting comment
+# This workflow is triggered after the linting action is complete
+# It posts an automated comment to the PR, even if the PR is coming from a fork
+
+on:
+  workflow_run:
+    workflows: ["nf-core linting"]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download lint results
+        uses: dawidd6/action-download-artifact@v2
+        with:
+          workflow: linting.yml
+
+      - name: Get PR number
+        id: pr_number
+        run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+
+      - name: Post PR comment
+        uses: marocchino/sticky-pull-request-comment@v2
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          number: ${{ steps.pr_number.outputs.pr_number }}
+          path: linting-logs/lint_results.md
+
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.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/rnaseq' }}
+    env:
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Build new docker image
+        run: docker build --no-cache . -t nfcore/rnaseq:dev
+
+      - name: Push Docker image to DockerHub (dev)
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker push nfcore/rnaseq:dev
diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
@@ -1,16 +1,13 @@
-name: nf-core Docker push
+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:
-  push:
-    branches:
-      - dev
   release:
     types: [published]
 
 jobs:
   push_dockerhub:
-    name: Push new Docker image to Docker Hub
+    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/rnaseq' }}
@@ -24,15 +21,7 @@ jobs:
       - name: Build new docker image
         run: docker build --no-cache . -t nfcore/rnaseq: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/rnaseq:latest nfcore/rnaseq:dev
-          docker push nfcore/rnaseq: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/rnaseq:latest
diff --git a/CHANGELOG.md b/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).
 
-## v1.4.3dev - [date]
+## v2.1dev - [date]
 
 Initial release of nf-core/rnaseq, created with the [nf-core](https://nf-co.re/) template.
 
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM nfcore/base:1.11
+FROM nfcore/base:1.12
 LABEL authors="Phil Ewels, Rickard Hammarén" \
       description="Docker image containing all software requirements for the nf-core/rnaseq pipeline"
 
@@ -7,10 +7,10 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-rnaseq-1.4.3dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-rnaseq-2.1dev/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-rnaseq-1.4.3dev > nf-core-rnaseq-1.4.3dev.yml
+RUN conda env export --name nf-core-rnaseq-2.1dev > nf-core-rnaseq-2.1dev.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile
diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 
 [![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rnaseq/actions)
 [![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnaseq/actions)
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.04.0-brightgreen.svg)](https://www.nextflow.io/)
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)
 [![Docker](https://img.shields.io/docker/automated/nfcore/rnaseq.svg)](https://hub.docker.com/r/nfcore/rnaseq)
diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt
@@ -14,7 +14,7 @@ Content-Transfer-Encoding: base64
 Content-ID: <nfcorepipelinelogo>
 Content-Disposition: inline; filename="nf-core-rnaseq_logo.png"
 
-<% out << new File("$baseDir/assets/nf-core-rnaseq_logo.png").
+<% out << new File("$projectDir/assets/nf-core-rnaseq_logo.png").
   bytes.
   encodeBase64().
   toString().
diff --git a/environment.yml b/environment.yml
@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-rnaseq-1.4.3dev
+name: nf-core-rnaseq-2.1dev
 channels:
   - conda-forge
   - bioconda
diff --git a/main.nf b/main.nf
@@ -92,10 +92,10 @@ if (workflow.profile.contains('awsbatch')) {
 }
 
 // Stage config files
-ch_multiqc_config = file("$baseDir/assets/multiqc_config.yaml", checkIfExists: true)
+ch_multiqc_config = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true)
 ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
-ch_output_docs = file("$baseDir/docs/output.md", checkIfExists: true)
-ch_output_docs_images = file("$baseDir/docs/images/", checkIfExists: true)
+ch_output_docs = file("$projectDir/docs/output.md", checkIfExists: true)
+ch_output_docs_images = file("$projectDir/docs/images/", checkIfExists: true)
 
 /*
  * Create a channel for input read files
@@ -326,18 +326,18 @@ workflow.onComplete {
 
     // Render the TXT template
     def engine = new groovy.text.GStringTemplateEngine()
-    def tf = new File("$baseDir/assets/email_template.txt")
+    def tf = new File("$projectDir/assets/email_template.txt")
     def txt_template = engine.createTemplate(tf).make(email_fields)
     def email_txt = txt_template.toString()
 
     // Render the HTML template
-    def hf = new File("$baseDir/assets/email_template.html")
+    def hf = new File("$projectDir/assets/email_template.html")
     def html_template = engine.createTemplate(hf).make(email_fields)
     def email_html = html_template.toString()
 
     // Render the sendmail template
-    def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir", mqcFile: mqc_report, mqcMaxSize: params.max_multiqc_email_size.toBytes() ]
-    def sf = new File("$baseDir/assets/sendmail_template.txt")
+    def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: params.max_multiqc_email_size.toBytes() ]
+    def sf = new File("$projectDir/assets/sendmail_template.txt")
     def sendmail_template = engine.createTemplate(sf).make(smail_fields)
     def sendmail_html = sendmail_template.toString()
 
diff --git a/nextflow.config b/nextflow.config
@@ -57,7 +57,7 @@ try {
 }
 
 profiles {
-  conda { process.conda = "$baseDir/environment.yml" }
+  conda { process.conda = "$projectDir/environment.yml" }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   docker {
     docker.enabled = true
@@ -75,6 +75,7 @@ profiles {
     podman.enabled = true
   }
   test { includeConfig 'conf/test.config' }
+  test_full { includeConfig 'conf/test_full.config' }
 }
 
 // Load igenomes.config if required
@@ -115,8 +116,8 @@ manifest {
   homePage = 'https://github.com/nf-core/rnaseq'
   description = 'Nextflow RNA-Seq analysis pipeline, part of the nf-core community.'
   mainScript = 'main.nf'
-  nextflowVersion = '>=19.10.0'
-  version = '1.4.3dev'
+  nextflowVersion = '>=20.04.0'
+  version = '2.1dev'
 }
 
 // Function to ensure that resource requirements don't go beyond
