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Fix herc2 workflow shell compatibility
Remove printf '%q' which is bash-specific but the container uses /bin/sh. The filename from Nextflow staging is already safe to use directly.
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examples/herc2/herc2-classifier/workflow.nf

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Original file line numberDiff line numberDiff line change
@@ -53,8 +53,7 @@ process herc2_classifier {
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script:
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def genoFileName = genotype_file.getName()
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"""
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GENO_FILE=\$(printf '%q' "${genoFileName}")
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bioscript classify "${assets_dir}/classify_herc2.py" --file \$GENO_FILE --participant_id "${participant_id}"
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bioscript classify "${assets_dir}/classify_herc2.py" --file "${genoFileName}" --participant_id "${participant_id}"
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"""
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}
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