convert_fai_to_seqinfo
Converts a FastA index (fai) to a {GenomeInfoDb} Seqinfo object and saves the object to an RDS file.
Inputs
| Channel name | Description | Type |
|---|---|---|
opt | A map of task-specific variables. | map |
tag | A unique identifier to use in the tag directive. | string |
genome | Name of the genome, eg “mm10 + GFP”. This is used to create the Seqinfo object. | string |
fai | Path to a FastA index file for the genome that the GTF is relevant to. This is used to create the Seqinfo object. | file |
Outputs
| Emission name | Description | Type | Filename pattern |
|---|---|---|---|
opt | A map of task-specific variables. | map | |
task | YAML-formatted file of task parameters and software versions used by the task. | file | task.yaml |
seqinfo | RDS obejct of a Seqinfo object. | file | seqinfo.rds |
Tools
genomeinfodb
Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.
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