When running tranquillyzer multiple times with the same output directory, the demuxed FASTA files demuxed.fasta and ambiguous.fasta are appended to, rather than overwritten. I believe this is also an issue when writing to FASTQs.
When rerunning tranquillyzer, I would assume that results of the previous run would be overwritten. The user could be prompted to know this is occurring (whether it's a warning and then it happens automatically or a check is performed and the user has to explicitly opt in by adding a --force flag or something is up for discussion).
There's also the added issue of what happens when the same data is processed with two different models but fed to the same output directory. Currently, the later run will append and/or overwrite (depending on the circumstance I presume other files are overwritten rather than appended to) the previous run. However, it's possible the user may want both runs to live side-by-side in the same directory.
When running tranquillyzer multiple times with the same output directory, the demuxed FASTA files
demuxed.fastaandambiguous.fastaare appended to, rather than overwritten. I believe this is also an issue when writing to FASTQs.When rerunning tranquillyzer, I would assume that results of the previous run would be overwritten. The user could be prompted to know this is occurring (whether it's a warning and then it happens automatically or a check is performed and the user has to explicitly opt in by adding a
--forceflag or something is up for discussion).There's also the added issue of what happens when the same data is processed with two different models but fed to the same output directory. Currently, the later run will append and/or overwrite (depending on the circumstance I presume other files are overwritten rather than appended to) the previous run. However, it's possible the user may want both runs to live side-by-side in the same directory.