Discrepancy in documentation and Tool description

[Rohit-Satyam]

Hi

I observe a small discrepancy in documentation

The tool description says, that -i option require either a single fastq file or a directory. But when I provide directory path containing multiple samples fastq files, I get the following error:

porechop_abi: error: unrecognized arguments: barcode82_sample_10.fastq barcode83_sample_1904.fastq barcode84_sample_1905.fastq barcode85_sample_441.fastq barcode86_sample_4447.fastq

Main options:
  -i INPUT, --input INPUT             FASTA/FASTQ of input reads or a directory which will be recursively
                                      searched for FASTQ files (required)

Lastly can you see if there is an option --multi_run in the tool as documentation says because when using it, I get the error:

porechop_abi: error: unrecognized arguments: --multi_run 10

or is this replaced by -nr/

[qbonenfant]

Hi, Thanks for reporting these issues. For the mr option, I have indeed forgot to replace the mr / multi-run flag by nr / number_of_run. It does the same thing as mr, it's just the option name that changed. I will edit the readme to match.

For the folder, this one comes directly from the original Porechop. You can not just give Porechop a list of file like this, it must be the folder they are in (Porechop will check if the input is a folder or a file by itself). One important thing to note: you can not run the -abi mode with a folder.

Why is that ? The reason Porechop support folders date from the Albacore basecaller. When using barcode, Albacore demultiplex the output in a folder with one file for each bin. Porechop can also do barcode demultiplexing, and can "check" the work of albacore, by reprocessing the whole folder. Since our addition is not barcode-oriented, we did not implement folder management in the core module.

[qbonenfant]

Hi, This issue is finally resolved by PR #15 (sorry it took so long). I will now close this issue. Thanks for your contribution to this project.