From 4b3c86ed9f428f97550a04cf035db92aa018abcd Mon Sep 17 00:00:00 2001 From: JoseEspinosa 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