Preseq testing

.github/workflows/preseq_lcextrap.yml

@@ -0,0 +1,40 @@
+name: preseq_lcextrap
+on:
+  push:
+    paths:
+      - software/preseq/lcextrap/**
+      - .github/workflows/preseq_lcextrap.yml
+      - tests/software/preseq/**
+  pull_request:
+    paths:
+      - software/preseq/lcextrap/**
+      - .github/workflows/preseq_lcextrap.yml
+      - tests/software/preseq/**
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      # Test the module
+      - run: pytest --tag preseq_lcextrap --symlink --wt 2

software/preseq/lcextrap/main.nf

@@ -37,7 +37,7 @@ process PRESEQ_LCEXTRAP {
         $options.args \\
         $paired_end \\
         -output ${prefix}.ccurve.txt \\
-        $bam
+        -bam $bam
     cp .command.err ${prefix}.command.log
 
     echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//' > ${software}.version.txt

tests/software/preseq/main.nf

@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PRESEQ_LCEXTRAP as PRESEQ_LCEXTRAP_SE } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [ publish_dir:'test_preseq_single_end' ] )
+include { PRESEQ_LCEXTRAP as PRESEQ_LCEXTRAP_PE } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [ publish_dir:'test_preseq_paired_end' ] )
+
+/*
+ * Test with single-end data
+ */
+
+workflow test_preseq_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1106616_5M_subset.bam', checkIfExists: true), ] ]
+
+    PRESEQ_LCEXTRAP_SE ( input )
+}
+
+/*
+ * Test with paired-end data
+ */
+
+workflow test_preseq_paired_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1106616_5M_subset.bam', checkIfExists: true), ] ]
+
+    PRESEQ_LCEXTRAP_PE ( input )
+}
+

tests/software/preseq/test.yml

@@ -0,0 +1,21 @@
+- name: Run preseq single-end lcextrap
+  command: nextflow run ./tests/software/preseq -profile docker -entry test_preseq_single_end -c tests/config/nextflow.config
+  tags:
+    - preseq
+    - preseq_lcextrap
+
+  files:
+    - path: output/test_preseq_single_end/test.ccurve.txt
+      md5sum: 5253ffcfd4b6162851631efdbfe16f92
+    - path: output/test_preseq_single_end/test.command.log
+
+- name: Run preseq paired-end lcextrap
+  command: nextflow run ./tests/software/preseq -profile docker -entry test_preseq_paired_end -c tests/config/nextflow.config
+  tags:
+    - preseq
+    - preseq_lcextrap
+
+  files:
+    - path: output/test_preseq_paired_end/test.ccurve.txt
+      md5sum: 66b339780630fc1aa72dcfbd0a4490fd
+    - path: output/test_preseq_paired_end/test.command.log