From c1ed4e21becc6450822445bae3b333e58c44158d Mon Sep 17 00:00:00 2001
From: Lucas Taniguti <lucas.taniguti@mendelics.com.br>
Date: Fri, 13 May 2022 07:42:34 -0300
Subject: [PATCH] tests: add haplocheck tests

---
 tests/config/pytest_modules.yml          | 12 ++++++++----
 tests/modules/haplocheck/main.nf         | 16 ++++++++++++++++
 tests/modules/haplocheck/nextflow.config |  5 +++++
 tests/modules/haplocheck/test.yml        | 13 +++++++++++++
 4 files changed, 42 insertions(+), 4 deletions(-)
 create mode 100644 tests/modules/haplocheck/main.nf
 create mode 100644 tests/modules/haplocheck/nextflow.config
 create mode 100644 tests/modules/haplocheck/test.yml

diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 9afe83fd..97732c05 100644
--- a/tests/config/pytest_modules.yml
+++ b/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/**
diff --git a/tests/modules/haplocheck/main.nf b/tests/modules/haplocheck/main.nf
new file mode 100644
index 00000000..86cc448e
--- /dev/null
+++ b/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 )
+}
diff --git a/tests/modules/haplocheck/nextflow.config b/tests/modules/haplocheck/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/haplocheck/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/haplocheck/test.yml b/tests/modules/haplocheck/test.yml
new file mode 100644
index 00000000..edfd2aba
--- /dev/null
+++ b/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