added nf-tests

- dry (stub) runs for each input type
  - input are empty files
- dry run ci test with nf-test

.github/workflows/dryrun.yml

@@ -0,0 +1,65 @@
+name: dry run CI
+
+env:
+  NXF_ANSI_LOG: false
+
+jobs:
+  test:
+    name: Dry run ${{ matrix.inputtype }}-${{ matrix.profile }} pipeline test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "23.04.1"
+          - "latest"
+        inputtype:
+          - fasta
+          - illumina
+          - nanopore
+        profile: ["docker"] # TODO , "singularity", "conda"]
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+
+      - uses: actions/cache@v2
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Install nf-test
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda clean
+        if: matrix.profile == 'conda'
+        run: conda clean -a
+
+      - name: Run nf-test
+        run: nf-test test --profile=${{ matrix.profile }} tests/${{ matrix.inputtype }}/*.nf.test --tap=test.tap
+
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap

.gitignore

@@ -11,3 +11,4 @@ centrifuge-cloud/
 conda/
 singularity/
 .vscode/
+.nf-test/

configs/test.config

@@ -0,0 +1,12 @@
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/
+params {
+    // Limit resources so that this can run on GitHub Actions
+    max_cores   = 2
+    cores = 1
+    max_memory = 6.GB
+    memory = 6.GB
+}

nf-test.config

@@ -0,0 +1,7 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "tests/nextflow.config"
+
+}

tests/fasta/main.nf.test

@@ -0,0 +1,24 @@
+nextflow_pipeline {
+
+    name "FASTA input"
+    script "../../clean.nf"
+
+    test("Stub") {
+        options "-stub-run"
+
+        when {
+            params {
+                input_type     = "fasta"
+                input      = "$projectDir/assets/EMPTY_FILE"
+                own = "$projectDir/assets/EMPTY_FILE"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+}

tests/illumina/main.nf.test

@@ -0,0 +1,80 @@
+nextflow_pipeline {
+
+    name "Illumina input"
+    script "../../clean.nf"
+
+    test("Stub paired-end") {
+        options "-stub-run"
+
+        when {
+            params {
+                input_type     = "illumina"
+                input      = "$projectDir/assets/EMPTY_FILE_{R1,R2}.fastq"
+                own = "$projectDir/assets/EMPTY_FILE"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Stub single-end") {
+        options "-stub-run"
+
+        when {
+            params {
+                input_type     = "illumina_single_end"
+                input      = "$projectDir/assets/EMPTY_FILE"
+                own = "$projectDir/assets/EMPTY_FILE"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Stub paired-end bbduk") {
+        options "-stub-run"
+
+        when {
+            params {
+                input_type     = "illumina"
+                input      = "$projectDir/assets/EMPTY_FILE_{R1,R2}.fastq"
+                own = "$projectDir/assets/EMPTY_FILE"
+                bbduk = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Stub single-end bbduk") {
+        options "-stub-run"
+
+        when {
+            params {
+                input_type     = "illumina_single_end"
+                input      = "$projectDir/assets/EMPTY_FILE"
+                own = "$projectDir/assets/EMPTY_FILE"
+                bbduk = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+}

tests/nanopore/main.nf.test

@@ -0,0 +1,24 @@
+nextflow_pipeline {
+
+    name "Nanopore input"
+    script "../../clean.nf"
+
+    test("Stub") {
+        options "-stub-run"
+
+        when {
+            params {
+                input_type     = "nano"
+                input      = "$projectDir/assets/EMPTY_FILE"
+                own = "$projectDir/assets/EMPTY_FILE"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+}