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add stubs for stranger (#1543)

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Ramprasad Neethiraj 2022-04-22 10:10:43 +02:00 committed by GitHub
parent 12afb6b0fa
commit c7329a3a57
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3 changed files with 26 additions and 0 deletions
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11
modules/stranger/main.nf
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@ -33,4 +33,15 @@ process STRANGER {
stranger: \$( stranger --version )
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
stranger: \$( stranger --version )
END_VERSIONS
"""
}

5
tests/modules/stranger/main.nf
View file

@ -23,3 +23,8 @@ workflow test_stranger_without_optional_variant_catalog {
EXPANSIONHUNTER ( input, fasta, variant_catalog )
STRANGER ( EXPANSIONHUNTER.out.vcf, [] )
}
workflow test_stranger_without_optional_variant_catalog_stubs {
EXPANSIONHUNTER ( input, fasta, variant_catalog )
STRANGER ( EXPANSIONHUNTER.out.vcf, [] )
}

10
tests/modules/stranger/test.yml
View file

@ -25,3 +25,13 @@
md5sum: bbe15159195681d5c18596d3ad85c78f
- path: output/stranger/versions.yml
md5sum: 8558542a007e90ea5dcdceed3f12585d
- name: stranger test_stranger_without_optional_variant_catalog_stubs
command: nextflow run tests/modules/stranger -entry test_stranger_without_optional_variant_catalog -c tests/config/nextflow.config -stub-run
tags:
- stranger
files:
- path: output/expansionhunter/test.vcf
- path: output/expansionhunter/versions.yml
- path: output/stranger/test.vcf.gz
- path: output/stranger/versions.yml