From 4b3c86ed9f428f97550a04cf035db92aa018abcd Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Tue, 23 Feb 2021 19:05:57 +0100
Subject: [PATCH] Add tests for bcftools-mpileup

---
 .github/filters.yml                      |  6 +++++-
 tests/software/bcftools/mpileup/main.nf  | 16 ++++++++++++++++
 tests/software/bcftools/mpileup/test.yml | 12 ++++++++++++
 3 files changed, 33 insertions(+), 1 deletion(-)
 create mode 100644 tests/software/bcftools/mpileup/main.nf
 create mode 100644 tests/software/bcftools/mpileup/test.yml

diff --git a/.github/filters.yml b/.github/filters.yml
index d8d63681..e726ed60 100644
--- a/.github/filters.yml
+++ b/.github/filters.yml
@@ -18,7 +18,11 @@ bcftools_merge:
   - software/bcftools/merge/**
   - tests/software/bcftools/merge/**
 
-bcftools_stats:
+bcftools_mpileup:
+  - software/bcftools/mpileup/**
+  - tests/software/bcftools/mpileup/**
+
+  bcftools_stats:
   - software/bcftools/stats/**
   - tests/software/bcftools/stats/**
 
diff --git a/tests/software/bcftools/mpileup/main.nf b/tests/software/bcftools/mpileup/main.nf
new file mode 100644
index 00000000..82bc3b23
--- /dev/null
+++ b/tests/software/bcftools/mpileup/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_MPILEUP } from '../../../../software/bcftools/mpileup/main.nf' addParams( options: ['args2': '--no-version --ploidy 1 --multiallelic-caller'] )
+
+workflow test_bcftools_mpileup {
+
+    def input = []
+    input = [ [ id:'test' ], // meta map
+              [ file("${launchDir}/tests/data/bam/test-sc2-artic-v3.bam", checkIfExists: true) ]]
+    fasta = [ file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true) ]
+
+    BCFTOOLS_MPILEUP ( input, fasta )
+
+}
diff --git a/tests/software/bcftools/mpileup/test.yml b/tests/software/bcftools/mpileup/test.yml
new file mode 100644
index 00000000..0f42b685
--- /dev/null
+++ b/tests/software/bcftools/mpileup/test.yml
@@ -0,0 +1,12 @@
+- name: bcftools mpileup
+  command: nextflow run ./tests/software/bcftools/mpileup -entry test_bcftools_mpileup -c tests/config/nextflow.config
+  tags:
+    - bcftools
+    - bcftools_mpileup
+  files:
+    - path: output/bcftools/test.vcf.gz
+      md5sum: cad164d4a83dc8fa0889198acc196ce0
+    - path: output/bcftools/test.vcf.gz.tbi
+      md5sum: 51f4c3c6eec17d54e8f793ba5ba7b350
+    - path: output/bcftools/test.bcftools_stats.txt
+      md5sum: e632d29778c2b95b8b6e28ffec6fe7dd