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Correct parsing versions with trailing zeros (#795)
* 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>
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3 changed files with 5 additions and 4 deletions
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@ -79,7 +79,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
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}
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}
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with open("$versions") as f:
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with open("$versions") as f:
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workflow_versions = yaml.safe_load(f) | module_versions
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workflow_versions = yaml.load(f, Loader=yaml.BaseLoader) | module_versions
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workflow_versions["Workflow"] = {
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workflow_versions["Workflow"] = {
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"Nextflow": "$workflow.nextflow.version",
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"Nextflow": "$workflow.nextflow.version",
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@ -17,8 +17,8 @@ workflow test_custom_dumpsoftwareversions {
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MULTIQC ( FASTQC.out.zip.collect { it[1] } )
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MULTIQC ( FASTQC.out.zip.collect { it[1] } )
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ch_software_versions = Channel.empty()
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ch_software_versions = Channel.empty()
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ch_software_versions = ch_software_versions.mix(FASTQC.out.version)
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ch_software_versions = ch_software_versions.mix(FASTQC.out.versions)
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ch_software_versions = ch_software_versions.mix(MULTIQC.out.version)
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ch_software_versions = ch_software_versions.mix(MULTIQC.out.versions)
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CUSTOM_DUMPSOFTWAREVERSIONS ( ch_software_versions.collectFile() )
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CUSTOM_DUMPSOFTWAREVERSIONS ( ch_software_versions.collectFile() )
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}
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}
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@ -13,7 +13,8 @@ def _get_workflow_names():
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here = Path(__file__).parent.resolve()
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here = Path(__file__).parent.resolve()
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pytest_workflow_files = here.glob("**/test.yml")
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pytest_workflow_files = here.glob("**/test.yml")
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for f in pytest_workflow_files:
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for f in pytest_workflow_files:
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test_config = yaml.safe_load(f.read_text())
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# test_config = yaml.safe_load(f.read_text())
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test_config = yaml.load(f.read_text(), Loader=yaml.BaseLoader)
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for workflow in test_config:
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for workflow in test_config:
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yield workflow["name"]
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yield workflow["name"]
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