Documentation for `readPaths`

[yfukai]

According to the example config files, I believe one should specify readPaths the parameter to process multiple samples at once (not the --reads option). It would be great if this feature is explicitly documented somewhere. Please let me know if I'm misunderstanding something about this.

[myoshimura080822]

For the standard use of ramdaq, we anticipate the use of the '-reads' option. This option allows for wildcard character, enabling you to run multiple files at once by specifying as follows:

Examples:

For SE: --reads "./fastq_files/*.fastq.gz"
For PE: --reads "./fastq_files/*{1,2}.fastq.gz"

Details : https://github.com/rikenbit/ramdaq/blob/master/docs/usage.md#--reads

Could you please confirm if my understanding of your question is correct?

[yfukai]

Thank you, I understand how the multiple 'file' scenarios will be handled. However, I'm unclear about applying this approach to cases involving multiple 'samples', such as instances where we already possess demultiplexed fastq files for each individual cell. Perhaps I'm overlooking something, but is there a method to manage these 'samples' scenarios using the --reads option?

[myoshimura080822]

Unfortunately, ramdaq does not yet have the concept of handling 'samples' at a higher file hierarchy level. I think the approach will either be to manage with the prefix of the filename, or to analyze the correspondence table of barcodes and samples as metadata.

[yfukai]

Thanks for your reply @myoshimura080822, maybe I'm misunderstanding something, but it looks like that ramdaq pipeline can align and summarize the fastq files separately if specified in readPaths. An example can be seen here which produces the attached MultiQC report. I think it would be helpful if this feature is explicitly documented.

[myoshimura080822]

Thank you for your valuable support. I suppose the attached table merges fastq files based on the prefix of the filenames for PE samples. We will verify this specification on our end and intend to include it in the documentation.