Creates a configuration file for a library, listing the sample names, assay types and paths to FastQ files (etc).
| Channel name | Description | Type |
|---|
opt | A map of task-specific variables. | map |
type | A hyphen-separated collection of assays, for example ‘10x-hto-vdj’, to determine the type of configuration file to produce. | string |
library ids | An array of library identifiers. These will be used to find the library type from the _project/library types map. | strings |
sample ids | A list of sample names that are expected in the library(s). | strings |
descriptions | A list of descriptions of the samples, added to the configuration file. | strings |
barcodes | A list of lists of barcodes for each sample. | strings |
feature types | An array of “Gene Expression” (etc) for each sample. | strings |
fastq path | An array of paths that contain FastQ files that could be added to the sample sheet. | paths |
index | A Cell Ranger (gene expression) index. Can be created with mkref or downloaded. | path |
index_vdj | A Cell Ranger (VDJ) index. Can be created with mkvdjref or downloaded. May be a non-existent path if not rewquired. | path |
probe_set.csv | A CSV file to map probes to genes. Can be downloaded from 10x. May be set to a non-existent file if not required. | file |
adt_set.csv | A CSV file that defines which sequenced tag is associated to which antibody. May be a non-existent file if not required. | file |
hto_set.csv | A CSV file that defines the sequences that identify barcodes. The reference in assets may be used. The file is subset for barcodes of samples in the library. | file |