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/ampliseq' }}
-  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/ampliseq' }}
+    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/ampliseq:latest
+      - name: Build new docker image
+        run: docker build --no-cache . -t nfcore/ampliseq: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/ampliseq:latest nfcore/ampliseq:dev
-        docker push nfcore/ampliseq: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/ampliseq:latest nfcore/ampliseq:dev
+          docker push nfcore/ampliseq:dev
 
-    - name: Push Docker image to DockerHub (release)
-      if: ${{ github.event_name == 'release' }}
-      run: |
-        echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-        docker push nfcore/ampliseq:latest
-        docker tag nfcore/ampliseq:latest nfcore/ampliseq:${{ github.event.release.tag_name }}
-        docker push nfcore/ampliseq:${{ github.event.release.tag_name }}
+      - name: Push Docker image to DockerHub (release)
+        if: ${{ github.event_name == 'release' }}
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker push nfcore/ampliseq:latest
+          docker tag nfcore/ampliseq:latest nfcore/ampliseq:${{ github.event.release.tag_name }}
+          docker push nfcore/ampliseq:${{ github.event.release.tag_name }}

Dockerfile

@@ -1,4 +1,4 @@
-FROM nfcore/base:1.10.1
+FROM nfcore/base:1.10.2
 LABEL authors="Daniel Straub, Alexander Peltzer" \
       description="Docker image containing all software requirements for the nf-core/ampliseq pipeline"
 

conf/test_full.config

@@ -15,7 +15,7 @@ params {
   // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
   // TODO nf-core: Give any required params for the test so that command line flags are not needed
   single_end = false
-  readPaths = [
+  input_paths = [
     ['Testdata', ['https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R1.tiny.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R2.tiny.fastq.gz']],
     ['SRR389222', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz']]
   ]

docs/usage.md

@@ -80,7 +80,7 @@ You can also supply a run name to resume a specific run: `-resume [run-name]`. U
 
 ### `-c`
 
-Specify the path to a specific config file (this is a core NextFlow command). See the [nf-core website documentation](https://nf-co.re/usage/configuration) for more information.
+Specify the path to a specific config file (this is a core Nextflow command). See the [nf-core website documentation](https://nf-co.re/usage/configuration) for more information.
 
 #### Custom resource requests
 

main.nf

@@ -127,7 +127,7 @@ def summary = [:]
 if (workflow.revision) summary['Pipeline Release'] = workflow.revision
 summary['Run Name']         = custom_runName ?: workflow.runName
 // TODO nf-core: Report custom parameters here
-summary['Reads']            = params.input
+summary['Input']            = params.input
 summary['Fasta Ref']        = params.fasta
 summary['Data Type']        = params.single_end ? 'Single-End' : 'Paired-End'
 summary['Max Resources']    = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"