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

Pretty sure this is passing it a sorted bam though?

software/samtools/sort/test/input/test.paired_end.name.sorted.bam

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

software/samtools/sort/test/main.nf

@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_SORT } from '../main.nf' addParams( options: [:] )
-
-workflow test {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              file("${baseDir}/input/test.paired_end.name.sorted.bam", checkIfExists: true) ]
-
-    SAMTOOLS_SORT ( input )
-}
-
-workflow {
-    test()
-}

software/samtools/sort/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

@@ -5,6 +5,7 @@ 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: [:] )
+include { SAMTOOLS_SORT } from '../../../software/samtools/sort/main.nf' addParams( options: [:] )
 
 workflow test_samtools_flagstat {
 
@@ -34,3 +35,13 @@ workflow test_samtools_index {
 
     SAMTOOLS_INDEX ( input )
 }
+
+// FIXME Why is this passing it an already sorted bam?
+workflow test_samtools_sort  {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+
+    SAMTOOLS_SORT ( input )
+}

tests/software/samtools/test.yml

@@ -24,3 +24,12 @@
   files:
     - path: output/samtools/test.paired_end.sorted.bam.bai
       md5sum: 67338c2995eae82c849830ca55aa7bd1
+
+- name: Run samtools sort test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_sort -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_sort
+  files:
+    - path: output/samtools/test.bam
+      md5sum: a41bfadacd2eeef1d31e05c135cc4f4e