test(samtools): Refactor flagstat to use pytest-workflow

.github/workflows/software/samtools_flagstat.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/samtools/flagstat/test/ -profile docker
+      - run: pytest --tag samtools_flagstat --symlink --wt 2

software/samtools/flagstat/test/input/test.paired_end.sorted.bam

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

software/samtools/flagstat/test/input/test.paired_end.sorted.bam.bai

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

software/samtools/flagstat/test/main.nf

@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_FLAGSTAT } 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.sorted.bam.bai", checkIfExists: true) ]
-
-    SAMTOOLS_FLAGSTAT ( input )
-}
-
-workflow {
-    test()
-}

software/samtools/flagstat/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
-    }
-}

software/samtools/flagstat/test/output/samtools/test.paired_end.sorted.bam.flagstat

@@ -1,13 +0,0 @@
-20000 + 0 in total (QC-passed reads + QC-failed reads)
-0 + 0 secondary
-0 + 0 supplementary
-0 + 0 duplicates
-20000 + 0 mapped (100.00% : N/A)
-20000 + 0 paired in sequencing
-10000 + 0 read1
-10000 + 0 read2
-20000 + 0 properly paired (100.00% : N/A)
-20000 + 0 with itself and mate mapped
-0 + 0 singletons (0.00% : N/A)
-0 + 0 with mate mapped to a different chr
-0 + 0 with mate mapped to a different chr (mapQ>=5)

tests/software/samtools/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_FLAGSTAT } from '../../../software/samtools/flagstat/main.nf' addParams( options: [:] )
+
+workflow test_samtools_flagstat {
+
+    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.sorted.bam.bai", checkIfExists: true) ]
+
+    SAMTOOLS_FLAGSTAT ( input )
+}

tests/software/samtools/test.yml

@@ -0,0 +1,8 @@
+- name: Run samtools flagstat test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_flagstat -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_flagstat
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.flagstat
+      md5sum: 80590621c74f5ee43ada20d010a3837f