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

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

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

software/samtools/index/test/main.nf

@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_INDEX } 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) ]
-
-    SAMTOOLS_INDEX ( input )
-}
-
-workflow {
-    test()
-}

software/samtools/index/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/samtools/main.nf

@@ -4,6 +4,7 @@ nextflow.enable.dsl = 2
 
 include { SAMTOOLS_FLAGSTAT } from '../../../software/samtools/flagstat/main.nf' addParams( options: [:] )
 include { SAMTOOLS_IDXSTATS } from '../../../software/samtools/idxstats/main.nf' addParams( options: [:] )
+include { SAMTOOLS_INDEX } from '../../../software/samtools/index/main.nf' addParams( options: [:] )
 
 workflow test_samtools_flagstat {
 
@@ -24,3 +25,12 @@ workflow test_samtools_idxstats {
 
     SAMTOOLS_IDXSTATS ( input )
 }
+
+workflow test_samtools_index {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+
+    SAMTOOLS_INDEX ( input )
+}

tests/software/samtools/test.yml

@@ -15,3 +15,12 @@
   files:
     - path: output/samtools/test.paired_end.sorted.bam.idxstats
       md5sum: 3bee8b7d55e412da2b3816c5a18d60d5
+
+- name: Run samtools index test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_index -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_index
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.bai
+      md5sum: 67338c2995eae82c849830ca55aa7bd1