Add tests for bcftools-mpileup

.github/filters.yml

@@ -18,6 +18,10 @@ bcftools_merge:
   - software/bcftools/merge/**
   - tests/software/bcftools/merge/**
 
+bcftools_mpileup:
+  - software/bcftools/mpileup/**
+  - tests/software/bcftools/mpileup/**
+
   bcftools_stats:
   - software/bcftools/stats/**
   - tests/software/bcftools/stats/**

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 )
+
+}

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