If directories for output do not exist, then output is absent, silently

[clintval]

I noticed if you include a directory in an output path, but that directory does not yet exist, then splitcode will proceed without warning and not create the directory nor create the output file(s).

You can reproduce this by modifying the command in the example documentation:

https://splitcode.readthedocs.io/en/latest/example.html#output-into-separate-files

splitcode -c config.txt --nFastqs=2 --assign \
    --output results/output_R1.fastq,results/output_R2.fastq \
    --unassigned=results/unassigned_R1.fastq,results/unassigned_R2.fastq \
    --outb=final_barcodes.fastq \
    --mapping=mapping.txt \
    --summary=summary.txt \
    R1.fastq R2.fastq

In the above, results/ will not be created and no files sent to that directory will exist, silently.

I would expect splitcode to make all directories (and their parents) if they did not exist.

[Yenaled]

Directories that don't exist are automatically created now -- version 0.31.6.