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Correct parsing versions with trailing zeros (#795)

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* Correct parsing versions with trailing zeros

* Fix test

* Update modules/custom/dumpsoftwareversions/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Fix tests and go back to output versions.yml

* Update tests/test_versions_yml.py to use BaseLoader

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
This commit is contained in:
Jose Espinosa-Carrasco 2021-10-06 08:16:36 +02:00 committed by GitHub
parent bcf2681b03
commit 84f2302920
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3 changed files with 5 additions and 4 deletions
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2
modules/custom/dumpsoftwareversions/main.nf
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@ -79,7 +79,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
} }
with open("$versions") as f: with open("$versions") as f:
workflow_versions = yaml.safe_load(f) | module_versions workflow_versions = yaml.load(f, Loader=yaml.BaseLoader) | module_versions
workflow_versions["Workflow"] = { workflow_versions["Workflow"] = {
"Nextflow": "$workflow.nextflow.version", "Nextflow": "$workflow.nextflow.version",

4
tests/modules/custom/dumpsoftwareversions/main.nf
View file

@ -17,8 +17,8 @@ workflow test_custom_dumpsoftwareversions {
MULTIQC ( FASTQC.out.zip.collect { it[1] } ) MULTIQC ( FASTQC.out.zip.collect { it[1] } )
ch_software_versions = Channel.empty() ch_software_versions = Channel.empty()
ch_software_versions = ch_software_versions.mix(FASTQC.out.version) ch_software_versions = ch_software_versions.mix(FASTQC.out.versions)
ch_software_versions = ch_software_versions.mix(MULTIQC.out.version) ch_software_versions = ch_software_versions.mix(MULTIQC.out.versions)
CUSTOM_DUMPSOFTWAREVERSIONS ( ch_software_versions.collectFile() ) CUSTOM_DUMPSOFTWAREVERSIONS ( ch_software_versions.collectFile() )
} }

3
tests/test_versions_yml.py
View file

@ -13,7 +13,8 @@ def _get_workflow_names():
here = Path(__file__).parent.resolve() here = Path(__file__).parent.resolve()
pytest_workflow_files = here.glob("**/test.yml") pytest_workflow_files = here.glob("**/test.yml")
for f in pytest_workflow_files: for f in pytest_workflow_files:
test_config = yaml.safe_load(f.read_text()) # test_config = yaml.safe_load(f.read_text())
test_config = yaml.load(f.read_text(), Loader=yaml.BaseLoader)
for workflow in test_config: for workflow in test_config:
yield workflow["name"] yield workflow["name"]