List fastq files — list_fastq_files • MiscMetabar

Useful for targets bioinformatic pipeline.

Usage

list_fastq_files(
  path,
  paired_end = TRUE,
  pattern = "fastq",
  pattern_R1 = "_R1_",
  pattern_R2 = "_R2_",
  nb_files = Inf
)

Arguments

path: path to files (required)
paired_end: do you have paired_end files? (default TRUE)
pattern: a pattern to filter files (passed on to list.files function).
pattern_R1: a pattern to filter R1 files (default "R1")
pattern_R2: a pattern to filter R2 files (default "R2")
nb_files: the number of fastq files to list (default FALSE)

Value

a list of one (single end) or two (paired end) list of files files are sorted by names (default behavior of list.files())

Author

Adrien Taudière

Examples

list_fastq_files(system.file("extdata", package = "MiscMetabar"))
#> $fnfs
#> [1] "/tmp/RtmpRFGNr7/temp_libpath4080f47fd7b7e/MiscMetabar/extdata/ex_R1_001.fastq.gz"
#> 
#> $fnrs
#> [1] "/tmp/RtmpRFGNr7/temp_libpath4080f47fd7b7e/MiscMetabar/extdata/ex_R2_001.fastq.gz"
#> 
list_fastq_files(system.file("extdata", package = "MiscMetabar"),
  paired_end = FALSE, pattern_R1 = ""
)
#> $fnfs
#> [1] "/tmp/RtmpRFGNr7/temp_libpath4080f47fd7b7e/MiscMetabar/extdata/ex.fastq"          
#> [2] "/tmp/RtmpRFGNr7/temp_libpath4080f47fd7b7e/MiscMetabar/extdata/ex_R1_001.fastq.gz"
#> [3] "/tmp/RtmpRFGNr7/temp_libpath4080f47fd7b7e/MiscMetabar/extdata/ex_R2_001.fastq.gz"
#>