modules/simpleaf_quant

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

List of input FastQ files for paired-end data.
Reads should be grouped by pairs.

Groovy Map containing index information

Folder containing the index files

Groovy Map containing txp2gene information

File mapping transcripts to genes.

Chemistry used for library preparation. It can be a string describing
the specific chemistry or the geometry of the barcode, UMI, and
mappable read. For example, “10xv2” and “10xv3” will apply the
appropriate settings for 10x Chromium v2 and v3 protocols,
respectively. Alternatively, you can provide a general geometry string
if your chemistry is not pre-registered. For example, instead of
”10xv2”, you could use “1{b[16]u[10]x:}2{r:}”, or instead of “10xv3”,
you could use “1{b[16]u[12]x:}2{r:}“.

Groovy Map containing whitelist information

Whitelist file containing valid cell barcodes. Optional.