Get GTF file path from YAML

Usage

getGtfFileFromYaml(yaml)

Arguments

yaml: list. YAML metadata.

Value

character(1) or NULL. File path if the file exists. NULL if the file does not exist.

Note

Updated 2022-03-07.

Author

Michael Steinbaugh

Examples

file <- file.path(bcbioBaseTestsUrl, "summary.yaml")
yaml <- import(file)
#> → Downloading <https://r.acidgenomics.com/testdata/bcbiobase/summary.yaml> to /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmprBcLWH/8eItNjQMoX-16965116437962/pipette-10f0e58e10a1d.yaml.
#> → Importing <https://r.acidgenomics.com/testdata/bcbiobase/summary.yaml> using yaml::`yaml.load_file()`.
x <- getGtfFileFromYaml(yaml)
#> bcbio GTF file:
#> /groups/bcbio/bcbio_dev/genomes/Mmusculus/mm10/rnaseq/ref-transcripts.gtf
#> ! bcbio GTF file is not accessible.
print(x)
#> NULL