test(picard): Refactor mergesamfiles to use pytest-workflow

.github/workflows/software/picard_mergesamfiles.yml

@@ -17,7 +17,6 @@ jobs:
     env:
       NXF_ANSI_LOG: false
     steps:
-
       - uses: actions/checkout@v2
 
       - name: Install Nextflow
@@ -26,5 +25,12 @@ jobs:
           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: nextflow run ./software/picard/mergesamfiles/test/ -profile docker
+      - run: pytest --tag picard_mergesamfiles --symlink --wt 2

software/picard/mergesamfiles/test/input/test.paired_end.COPY.sorted.bam

@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam

software/picard/mergesamfiles/test/input/test.paired_end.sorted.bam

@@ -1 +0,0 @@
-../../../../../tests/data/bam/test.paired_end.sorted.bam

software/picard/mergesamfiles/test/main.nf

@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_MERGESAMFILES } from '../main.nf' addParams( options: [:] )
-
-workflow test {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
-                file("${baseDir}/input/test.paired_end.COPY.sorted.bam", checkIfExists: true), ] ]
-
-    PICARD_MERGESAMFILES ( input )
-}
-
-workflow {
-    test()
-}

software/picard/mergesamfiles/test/nextflow.config

@@ -1,20 +0,0 @@
-
-params {
-    outdir = "output/"
-    publish_dir_mode = "copy"
-    enable_conda = false
-}
-
-profiles {
-    conda  {
-        params.enable_conda = true
-    }
-    docker {
-        docker.enabled = true
-        docker.runOptions = '-u \$(id -u):\$(id -g)'
-    }
-    singularity {
-        singularity.enabled = true
-        singularity.autoMounts = true
-    }
-}

tests/software/picard/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_MERGESAMFILES } from '../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] )
+
+workflow test_picard_mergesamfiles {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true), ] ]
+
+    PICARD_MERGESAMFILES ( input )
+}

tests/software/picard/test.yml

@@ -0,0 +1,8 @@
+- name: Run picard mergesamfiles
+  command: nextflow run ./tests/software/picard -profile docker -entry test_picard_mergesamfiles -c tests/config/nextflow.config
+  tags:
+    - picard
+    - picard_mergesamfiles
+  files:
+    - path: output/picard/test.bam
+      md5sum: a9c8a28d1aac362df5973ba2d9923f86