Add and fix ECLint in pipeline

.editorconfig

@@ -0,0 +1,24 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{yml,yaml}]
+indent_size = 2
+
+# These files are edited upstream in nf-core/modules
+[/modules/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
+
+[/assets/email*]
+indent_size = unset

.github/PULL_REQUEST_TEMPLATE.md

@@ -16,8 +16,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/vira
 
 - [ ] 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/nf-core/viralrecon/tree/master/.github/CONTRIBUTING.md)
-  - [ ] If necessary, also make a PR on the nf-core/viralrecon _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/viralrecon/tree/master/.github/CONTRIBUTING.md)
+    - [ ] If necessary, also make a PR on the nf-core/viralrecon _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/ci.yml

@@ -1,138 +1,154 @@
-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:
-    branches:
-      - dev
-  pull_request:
-  release:
-    types: [published]
-
-jobs:
-  test:
-    name: Run workflow tests
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: ${{ matrix.nxf_ver }}
-      NXF_ANSI_LOG: false
-    strategy:
-      matrix:
-        # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: [21.04.0]
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with test data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
-
-  parameters:
-    name: Test workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: '21.04.0'
-      NXF_ANSI_LOG: false
-    strategy:
-      matrix:
-        parameters: [--skip_fastp, --skip_variants, --skip_cutadapt, --skip_kraken2, --skip_assembly, '--spades_mode corona', '--spades_mode metaviral']
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
-
-  test_sra:
-    name: Test SRA workflow
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: '21.04.0'
-      NXF_ANSI_LOG: false
-    strategy:
-      matrix:
-        parameters: [--skip_sra_fastq_download, '']
-
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline to download SRA ids and various options
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_sra,docker ${{ matrix.parameters }}
-
-  test_sispa:
-    name: Test SISPA workflow
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: '21.04.0'
-      NXF_ANSI_LOG: false
-    strategy:
-      matrix:
-        parameters: [--gff false, "--genome 'NC_045512.2'"]
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with minimal SISPA data and various options
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_sispa,docker ${{ matrix.parameters }}
-
-  test_nanopore:
-    name: Test Nanopore workflow
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}
-    runs-on: ubuntu-latest
-    env:
-      NXF_VER: '21.04.0'
-      NXF_ANSI_LOG: false
-    strategy:
-      matrix:
-        parameters: [--gff false, --input false, --min_barcode_reads 10000, --min_guppyplex_reads 10000, "--artic_minion_caller medaka"]
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with minimal Nanopore data and various options
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_nanopore,docker ${{ matrix.parameters }}
+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:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
+
+jobs:
+  test:
+    name: Run workflow tests
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}
+    runs-on: ubuntu-latest
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        # Nextflow versions: check pipeline minimum and current latest
+        nxf_ver: [21.04.0, ""]
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline with test data
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+
+  parameters:
+    name: Test workflow parameters
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}
+    runs-on: ubuntu-latest
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        parameters:
+          [
+            --skip_fastp,
+            --skip_variants,
+            --skip_cutadapt,
+            --skip_kraken2,
+            --skip_assembly,
+            "--spades_mode corona",
+            "--spades_mode metaviral",
+          ]
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline with various parameters
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
+
+  test_sra:
+    name: Test SRA workflow
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}
+    runs-on: ubuntu-latest
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        parameters: [--skip_sra_fastq_download, ""]
+
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline to download SRA ids and various options
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_sra,docker ${{ matrix.parameters }}
+
+  test_sispa:
+    name: Test SISPA workflow
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}
+    runs-on: ubuntu-latest
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        parameters: [--gff false, "--genome 'NC_045512.2'"]
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline with minimal SISPA data and various options
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_sispa,docker ${{ matrix.parameters }}
+
+  test_nanopore:
+    name: Test Nanopore workflow
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}
+    runs-on: ubuntu-latest
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        parameters:
+          [
+            --gff false,
+            --input false,
+            --min_barcode_reads 10000,
+            --min_guppyplex_reads 10000,
+            "--artic_minion_caller medaka",
+          ]
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline with minimal Nanopore data and various options
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_nanopore,docker ${{ matrix.parameters }}