Fix qc=none to automatically unzip gzipped input files#13
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When qc=none is used with gzipped input files (.gz extension), hyb now correctly unzips them before processing. Previously, qc=none would create a symlink directly to the compressed file, causing downstream tools to fail. The fix changes the qc=none preprocessing rule to depend on $(read) instead of $(in). This triggers the existing gunzip rule when the input is compressed, while maintaining backward compatibility with already-unzipped files. Tested with: - Gzipped FASTQ input: Successfully unzips and processes - Unzipped FASTQ input: Works as before (no unnecessary operations) - Full hyb analyse pipeline with vienna folding: Both cases complete successfully
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When qc=none is used with gzipped input files (.gz extension), hyb now correctly unzips them before processing. Previously, qc=none would create a symlink directly to the compressed file, causing downstream tools to fail.
The fix changes the qc=none preprocessing rule to depend on
$(read)instead of$(in). This triggers the existing gunzip rule when the input is compressed, while maintaining backward compatibility with already-unzipped files.Tested with: