Merge branch 'release/0.8.0'

.cspell.json

@@ -0,0 +1,22 @@
+{
+    "version": "0.2",
+    "language": "en",
+    "words": [
+        "CACHEDIR",
+        "Charliecloud",
+        "conda",
+        "entrez",
+        "ksumngs",
+        "MAFFT",
+        "metagenomic",
+        "NCBI",
+        "Nextflow",
+        "outdir",
+        "Palinski",
+        "phylotree",
+        "taxid",
+        "Trimmomatic",
+        "yavsap",
+        "Zenodo"
+    ]
+}

.editorconfig

@@ -1,4 +1,3 @@
-
 root = true
 
 [*]
@@ -9,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js,pug,rst,prettierrc}]
+[*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules

.gitattributes

@@ -1 +1,4 @@
 *.config linguist-language=nextflow
+modules/nf-core/** linguist-generated
+subworkflows/nf-core/** linguist-generated
+bin/sequence-table linguist-language=julia

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,51 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: ["bug"]
+title: "[Bug]: "
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Before you post this issue, please check the documentation:
+
+        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
+        - [yavsap pipeline documentation](https://ksumngs.github.io/yavsap/usage)
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: |
+        $ nextflow run ...
+
+        Some output where something broke
+
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: |
+        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Nextflow version _(eg. 21.10.3)_
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+        * Executor _(eg. slurm, local, awsbatch)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+        * Version of nf-core/yavsap _(eg. 1.1, 1.5, 1.8.2)_

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,28 @@
+name: Feature request
+description: Suggest an idea for the nf-core/yavsap pipeline
+labels: ["enhancement"]
+title: "[Feature]: "
+body:
+  - type: textarea
+    id: summary
+    attributes:
+      label: Summary of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true
+  - type: textarea
+    id: processes
+    attributes:
+      label: Additional processes
+      description: Explain what tools would be needed to implement this feature, along with a link to the tool's documentation and a container for the tool.
+  - type: textarea
+    id: parameters
+    attributes:
+      label: Additional parameters
+      description: Give a list of new parameters and which tools/processes it would be passed to
+  - type: textarea
+    id: visualizer
+    attributes:
+      label: Additional visualizer section
+      description: Describe a new section to add to the visualizer
+      placeholder:

.github/PULL_REQUEST_TEMPLATE.md

@@ -17,14 +17,11 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/ksumngs/yavs
 
 - [ ] 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 - have you followed the pipeline conventions
-        in the
-        [contribution docs](https://github.com/ksumngs/yavsap/tree/master/.github/CONTRIBUTING.md)
+  - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/ksumngs/yavsap/tree/master/.github/CONTRIBUTING.md)
+  - [ ] If necessary, also make a PR on the yavsap _branch_ on the [ksumngs/nf-test-datasets](https://github.com/ksumngs/nf-test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes
-      (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.
-- [ ] `README.md` is updated (including new tool citations and
-      authors/contributors).
+- [ ] `README.md` is updated (including new tool citations and authors/contributors).

.github/workflows/awsfulltest.yml

@@ -0,0 +1,33 @@
+name: nf-core AWS full size tests
+# This workflow is triggered on published releases.
+# It can be additionally triggered manually with GitHub actions workflow dispatch button.
+# It runs the -profile 'test_full' on AWS batch
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+jobs:
+  run-tower:
+    name: Run AWS full tests
+    if: github.repository == 'nf-core/yavsap'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Launch workflow via tower
+        uses: nf-core/tower-action@v3
+        # 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)
+        # on the `test_full.config` test runs with only one set of parameters
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/yavsap/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/yavsap/results-${{ github.sha }}"
+            }
+          profiles: test_full,aws_tower
+          nextflow_config: |
+            process.errorStrategy = 'retry'
+            process.maxRetries = 3

.github/workflows/awstest.yml

@@ -0,0 +1,28 @@
+name: nf-core AWS test
+# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
+# It runs the -profile 'test' on AWS batch
+
+on:
+  workflow_dispatch:
+jobs:
+  run-tower:
+    name: Run AWS tests
+    if: github.repository == 'nf-core/yavsap'
+    runs-on: ubuntu-latest
+    steps:
+      # Launch workflow using Tower CLI tool action
+      - name: Launch workflow via tower
+        uses: nf-core/tower-action@v3
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/yavsap/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/yavsap/results-test-${{ github.sha }}"
+            }
+          profiles: test,aws_tower
+          nextflow_config: |
+            process.errorStrategy = 'retry'
+            process.maxRetries = 3

.github/workflows/branch.yml

@@ -42,3 +42,4 @@ jobs:
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
+#

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: Testing
+name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
   push:
@@ -15,7 +15,7 @@ env:
 
 jobs:
   test:
-    name: Run workflow tests
+    name: Run pipeline with test data
     # Only run on push if this is the develop branch (merged PRs)
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'ksumngs/yavsap') }}
     runs-on: ubuntu-latest
@@ -24,8 +24,9 @@ jobs:
         # Nextflow versions
         include:
           # Test pipeline minimum Nextflow version
-          - NXF_VER: "21.10.6"
+          - NXF_VER: "21.10.3"
             NXF_EDGE: ""
+          # Test latest edge release of Nextflow
           - NXF_VER: ""
             NXF_EDGE: "1"
     steps:
@@ -46,7 +47,7 @@ jobs:
         env:
           NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }}
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,gh,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile test,gh,docker --outdir results
 
   parameters:
     name: Test workflow parameters
@@ -84,7 +85,7 @@ jobs:
         env:
           NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }}
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,gh,docker ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,gh,docker ${{ matrix.parameters }} --outdir results
 
   test_interleaved:
     name: Test Interleaved Reads Workflow
@@ -104,7 +105,8 @@ jobs:
         env:
           NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }}
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_interleaved,gh,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile test_interleaved,gh,docker --outdir results
+
   test_nanopore:
     name: Run workflow tests
     # Only run on push if this is the develop branch (merged PRs)
@@ -123,4 +125,4 @@ jobs:
         env:
           NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }}
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,gh,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile test,gh,docker --outdir results

.github/workflows/docs.yml

@@ -17,16 +17,15 @@ jobs:
           requirements: docs/requirements.txt
       - name: Install nf-core Tools 🍎
         run: |
-          python -m pip install git+https://github.com/krokicki/tools@dev
+          python -m pip install nf-core
       - name: Convert schema to docs 🧑‍⚖️
         run: |
-          echo "# Complete Parameter Reference" > docs/parameters.md
-          echo "" >> docs/parameters.md
-          echo "Every single parameter in the entire pipeline is described here. If you need to" >> docs/parameters.md
-          echo "tweak every little detail of how your JEV samples are analyzed, you've come to" >> docs/parameters.md
-          echo "the right place! Note that *every* parameter is described here, even those that" >> docs/parameters.md
-          echo "shouldn't be used, so proceed with caution!" >> docs/parameters.md
-          nf-core schema docs nextflow_schema.json | tail -n+4 >> docs/parameters.md
+          nf-core schema docs -f \
+            -o docs/parameters.md \
+            -x markdown \
+            -c 'parameter,description,type,required,default'
+          sed -i '1s/^.*/# Complete Parameter Reference/' docs/parameters.md
+          sed -i "3s/^.*/Every single parameter in the entire pipeline is described here. If you need to tweak every little detail of how your samples are analyzed, you've come to the right place! Note that *every* parameter is described here, even those that shouldn't be used, so proceed with caution!/" docs/parameters.md
       - name: Build docs 📝
         run: |
           sphinx-build -b html docs docs/_build

.github/workflows/linting.yml

@@ -1,6 +1,7 @@
 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
+# It runs the `nf-core lint` and markdown lint tests to ensure
+# that the code meets the nf-core guidelines.
 on:
   push:
   pull_request:
@@ -19,7 +20,7 @@ jobs:
         run: npm install -g editorconfig-checker
 
       - name: Run ECLint check
-        run: editorconfig-checker -exclude '.*.md' $(git ls-files | grep -v test)
+        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
 
   Prettier:
     runs-on: ubuntu-latest
@@ -77,3 +78,5 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
+
+#

.github/workflows/linting_comment.yml

@@ -26,3 +26,4 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
           path: linting-logs/lint_results.md
+#