modules/simpleaf_quant

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

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:}”. Details at https://hackmd.io/@PI7Og0l1ReeBZu_pjQGUQQ/rJMgmvr13

Groovy Map containing index information e.g. [ tool:‘piscem’ ]

Folder containing the index files. For a *.almon*.index that is not generated by simpleaf to be taken, ‘—no-piscem’ MUST be specified in ext.args.

Groovy Map containing txp2gene information e.g. [ mode:‘usa’ ]

Cell filtering mode. Possible values are ‘usa’ and ‘whitelist’. ‘usa’ will use the default cell filtering mode, while ‘whitelist’ will use the whitelist file provided in the ‘whitelist’ input.

Number of cell barcodes to use for cell filtering. Set as empty (’[]’) unless ‘cell_filter’ is set to ‘forced-cells’ or ‘expect-cells’.

Groovy Map containing existing mapping results. e.g. [ tool:‘piscem’ ]