Good Afternoon! I am attempting to run the scrnaseq pipeline on an inDropsv3 dataset, but am having trouble finding the correct format for my sample sheet. I am inheriting this data from a few years back, and as such, am just interpreting what I can from the files given to me. There are 4 fastq files associated with each sample, which leads me to conclude the version chemistry. However, from what I learned online, the scrnaseq pipeline's kallisto functionality only allows for 2 fstq files input per sample, which obviously doesn't match up with the data I am seeing. Is there perhaps a dev branch of the pipeline or an older branch that is compatible with this data format? Thank you!

Hi, @Markus! Slack uses channels to organise discussions. Press the

...

more option on the left sidebar. Then hover over Your organisation, and finally select Channels to browse. Each nf-core pipeline has it’s own channel (e.g. #CE8SSJV3N). Please post any questions about specific pipelines in the relevant channel. If you’re not sure where to post your message, please ask @Rike Hanssen for help.

Best to ask in #CHN5BV5DW 🙂

Will do!