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| import pysam | ||
| from variant_extractor import VariantExtractor | ||
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| vcf_in = pysam.VariantFile("${vcf}") | ||
| header = str(vcf_in.header).rstrip("\\n") | ||
| vcf_in.close() | ||
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| extractor = VariantExtractor( | ||
| "${vcf}", | ||
| pass_only=${pass_only}, | ||
| ensure_pairs=${ensure_pairs} | ||
| ) | ||
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| with open("${prefix}.extracted.vcf", "w") as out: | ||
| out.write(header + "\\n") | ||
| for variant_record in extractor: | ||
| out.write(str(variant_record) + "\\n") | ||
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| extractor.close() | ||
| PYEOF |
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Please use a template for this. There are a few examples in modules if you search for template such as the module ANNDATA_BARCODES.
You might need to remove the def before the variables so the python script can access the groovy variable values.
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PR checklist
Closes #9996
topic: versions- See version_topicslabelnf-core modules test variantextractor --profile dockernf-core modules test variantextractor --profile singularitynf-core modules test variantextractor --profile condaDescription
Add new module for
variant-extractor(EUCANCan), a Python library fordeterministic extraction and homogenization of SNVs, indels and structural
variants (SVs) from VCF files.
The tool has no CLI — the module wraps the Python API directly via an inline
python3script usingpysam+VariantExtractor.Related: nf-core/variantbenchmarking#264