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

List of input FastQ files for paired-end data. Reads should be grouped by pairs. For example, [ [R1_1.fastq.gz, R2_1.fastq.gz], [R1_2.fastq.gz, R2_2.fastq.gz] ]

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

Folder containing the index files. For a salmon index that is not generated by simpleaf to be taken, '--no-piscem' MUST be specified in ext.args.

File mapping transcripts to genes. It can be either a two-column TSV file for a standard transcriptomic index containing the transcript-to-gene ID mapping information, or a three-column TSV file for an augmented transcriptomic index with the third column representing the splicing status of each transcript.

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'.

File containing a list of cell barcodes to use for cell filtering. Set as empty ('[]') unless 'cell_filter' is set to 'unfiltered-pl' or 'explicit-pl'.

UMI resolution (https://alevin-fry.readthedocs.io/en/latest/quant.html). Possible values are 'cr-like', 'cr-like-em', 'parsimony', 'parsimony-em', 'parsimony-gene', and 'parsimony-gene-em'.

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

Folder containing the existing mapping results. It must be generated by simpleaf or alevin-fry, and contain the mapping file named map.rad.

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

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

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

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

File containing software versions