Specify read files not on CWD

[fgvieira]

Is it possible to specify reads files that are not in the current working directory?

[lcoombe]

Hi @fgvieira,

Currently, the reads files need to be in the current working directory, as the driver script will search this directory for input reads files with the supplied prefix. You can always make soft-links to the reads if they are located elsewhere.

Hope that helps - thank you for your interest in ntEdit! Lauren

[fgvieira]

I want to run ntEdit as part as a bigger workflow, and it would be nice to be able to directly refer to the reads files, just like with the drafts file. Would it be possible to either:

• specify the reads files directly (e.g. --reads /path/to/file_R1.fq.gz /path/to/file_R2.fq.gz /path/to/file_other.fq.gz)
• allow the prefix to include a path (e.g. --reads /path/to/file). Something like:

  [file for file in Path('.').glob(f"{reads_prefix}*") if file.endswith((".fq", ".fq.gz", ".fastq", ".fastq.gz", ".fa", ".fa.gz", ".fasta", ".fasta.gz"))]