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tests: add stub

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This commit is contained in:
Lucas Taniguti 2022-06-08 08:46:22 -03:00
parent f26979c44e
commit abaec30889
2 changed files with 26 additions and 5 deletions
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16
modules/haplocheck/main.nf
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@ -11,9 +11,9 @@ process HAPLOCHECK {
tuple val(meta), path(vcf) tuple val(meta), path(vcf)
output: output:
tuple val(meta), path("*.txt"), emit: txt tuple val(meta), path("*.txt") , emit: txt
tuple val(meta), path("*.html"), emit: html tuple val(meta), path("*.html"), emit: html
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
@ -29,4 +29,16 @@ process HAPLOCHECK {
haplocheck: \$(echo \$(haplocheck --version 2>&1) | cut -f 2 -d " " ) haplocheck: \$(echo \$(haplocheck --version 2>&1) | cut -f 2 -d " " )
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch $prefix.txt
touch $prefix.html
cat <<-END_VERSIONS > versions.yml
"${task.process}":
haplocheck: \$(echo \$(haplocheck --version 2>&1) | cut -f 2 -d " " )
END_VERSIONS
"""
} }

15
tests/modules/haplocheck/test.yml
View file

@ -1,11 +1,20 @@
- name: "haplocheck" - name: haplocheck test_haplocheck
command: nextflow run ./tests/modules/haplocheck -entry test_haplocheck -c ./tests/config/nextflow.config -c ./tests/modules/haplocheck/nextflow.config command: nextflow run ./tests/modules/haplocheck -entry test_haplocheck -c ./tests/config/nextflow.config -c ./tests/modules/haplocheck/nextflow.config
tags: tags:
- "haplocheck" - haplocheck
files: files:
- path: "output/haplocheck/test.html" - path: output/haplocheck/test.html
md5sum: 59d69052c86edff0301816956eaf4d5f md5sum: 59d69052c86edff0301816956eaf4d5f
- path: output/haplocheck/test.raw.txt - path: output/haplocheck/test.raw.txt
md5sum: 69f4e5b28a59b97fc19eb8e8b650d9d5 md5sum: 69f4e5b28a59b97fc19eb8e8b650d9d5
- path: output/haplocheck/versions.yml - path: output/haplocheck/versions.yml
md5sum: 94e2fa3ceb3946487319f92cea08c942 md5sum: 94e2fa3ceb3946487319f92cea08c942
- name: haplocheck test_haplocheck using stubs
command: nextflow run ./tests/modules/haplocheck -entry test_haplocheck -c ./tests/config/nextflow.config -c ./tests/modules/haplocheck/nextflow.config -stub-run
tags:
- haplocheck
files:
- path: output/haplocheck/test.html
- path: output/haplocheck/test.raw.txt
- path: output/haplocheck/versions.yml