Hi people! Can anyone remind me if it is possible to run "bacass" on a short reads sample that was sequenced twice (in order to increase its coverage) without having to concatenate the FastQ files to pass them as input? I tried without success things like:

# Attempt 1
ID	R1	R2	LongFastQ	Fast5	GenomeSize
shortreads	/path/to/bac.R1.fastq.gz,/path/to/bac_reseq.R1.fastq.gz	/path/to/bac.R2.fastq.gz,/path/to/bac_reseq.R2.fastq.gz	NA	NA	NA

# Attempt 2
ID	R1	R2	LongFastQ	Fast5	GenomeSize
shortreads	/path/to/bac.R1.fastq.gz	/path/to/bac.R2.fastq.gz	NA	NA	NA
shortreads	/path/to/bac_reseq.R1.fastq.gz	/path/to/bac_reseq.R2.fastq.gz	NA	NA	NA

Thanks in advance for any help.

I have just created an issue to implement this step (I thought that it was already covered in the pipeline). I am going to try to accomplish it this week, but feel free to contribute vía PR (https://github.com/nf-core/bacass/blob/2.3.1/.github/CONTRIBUTING.md)🙂 .

Also very interested in this! Excited to see this added to the pipeline 🙂

@Santiago @Steph Smith I have just pushed this feature 😅 . It would be great you could contribute to the review process and the remaining issues as well. https://github.com/nf-core/bacass/pull/158

@Daniel_VM Will test and share feedback, thank you!!