Add support for subdir configuration #4
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standage
commented
Nov 5, 2025
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| copier.copy_files(workdir / "seq") | ||
| copier.copy_files(workdir / subdir) | ||
| copier.print_copy_log() | ||
| nlogs = len(list((workdir / "seq").glob("copy-log-*.toml"))) | ||
| with open(workdir / "seq" / f"copy-log-{nlogs + 1}.toml", "w") as fh: | ||
| nlogs = len(list((workdir / subdir).glob("copy-log-*.toml"))) | ||
| with open(workdir / subdir / f"copy-log-{nlogs + 1}.toml", "w") as fh: |
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| "-s", | ||
| "--subdir", | ||
| metavar="PATH", | ||
| default="seq", | ||
| help="subdirectory path under --workdir to which sequence files will be written; PATH=`seq` by default, but can contain nesting (e.g. `seq/study`)", |
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| parser = ArgumentParser(description="Copy FASTQ files and update sample names") | ||
| parser = ArgumentParser( | ||
| description="Copy FASTQ files and use sample names to make filenames consistent", | ||
| formatter_class=RichHelpFormatter, | ||
| ) |
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Did a CLI glow-up while I was at it.
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Looks good! |
rnmitchell
approved these changes
Nov 5, 2025
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