tests: add haplocheck tests

tests/config/pytest_modules.yml

@@ -895,6 +895,10 @@ hamronization/summarize:
   - modules/hamronization/summarize/**
   - tests/modules/hamronization/summarize/**
 
+haplocheck:
+  - modules/haplocheck/**
+  - tests/modules/haplocheck/**
+
 happy/happy:
   - modules/happy/happy/**
   - tests/modules/happy/happy/**
@@ -1643,14 +1647,14 @@ samtools/bam2fq:
   - modules/samtools/bam2fq/**
   - tests/modules/samtools/bam2fq/**
 
-samtools/convert:
-  - modules/samtools/convert/**
-  - tests/modules/samtools/convert/**
-
 samtools/collatefastq:
   - modules/samtools/collatefastq/**
   - tests/modules/samtools/collatefastq/**
 
+samtools/convert:
+  - modules/samtools/convert/**
+  - tests/modules/samtools/convert/**
+
 samtools/depth:
   - modules/samtools/depth/**
   - tests/modules/samtools/depth/**

tests/modules/haplocheck/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HAPLOCHECK } from '../../../modules/haplocheck/main.nf'
+
+workflow test_haplocheck {
+
+    input = [
+        [ id:'test' ], // meta map
+        // TODO: change to "params.test_data[]"
+        file("https://github.com/nf-core/test-datasets/raw/5101234ce48c3eb08adeed922e30a6e57e4fe5fb/testdata/NA12878_chrM.vcf.gz", checkIfExists: true)
+    ]
+
+    HAPLOCHECK ( input )
+}

tests/modules/haplocheck/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}

tests/modules/haplocheck/test.yml

@@ -0,0 +1,13 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml haplocheck
+- name: "haplocheck"
+  command: nextflow run ./tests/modules/haplocheck -entry test_haplocheck -c ./tests/config/nextflow.config -c ./tests/modules/haplocheck/nextflow.config
+  tags:
+    - "haplocheck"
+  files:
+    - path: "output/haplocheck/test.html"
+      md5sum: 59d69052c86edff0301816956eaf4d5f
+    - path: output/haplocheck/test.raw.txt
+      md5sum: 69f4e5b28a59b97fc19eb8e8b650d9d5
+    - path: output/haplocheck/versions.yml
+      md5sum: 94e2fa3ceb3946487319f92cea08c942