symlink.raw.fastqs: Create symlinks to fastq(.gz) files

In kstagaman/sharpton-lab-metaGTx.processing: Sharpton Lab Metagenomic & Metatranscriptomic Processing

Create symlinks to fastq(.gz) files

Description

This function creates symlinks in the current directory to fastq OR fastq.gz files in the provided directory.

Usage

symlink.raw.fastqs(
  fastq.dirs,
  delim,
  sample.field,
  pattern = "lane.*fastq\\.gz",
  split = "--",
  replacements = NULL,
  save.sample.names = TRUE
)

Arguments

fastq.dirs	character; path to raw FASTQs directory or a named vector of paths to raw FASTQs directories. If a vector, function will preppend name of path to sample names to keep them distinct.
delim	character; delimiter for finding sample names in fastq file names.
sample.field	integer; field (after cutting) in which to find sample names.
pattern	character; matching pattern for files you want to link. Default is 'lane.*fastq\.gz'.
split	character; character(s) to split the sample name from the read ID in link name, e.g. sample01-R1.fastq.gz OR sample01–R1.fastq.gz. Default is '–'".
replacements	list; a named list of patterns and replacements for file names, e.g. =list(to.replace = c("A", "B"), replace.by = c("a", "b")). Default is NULL.
save.sample.names	logical, whether to grab sample names from file names (TRUE) let user supply sample names directly (FALSE). Default is TRUE.

See Also

system, str_split, list.files, create.processing.env

kstagaman/sharpton-lab-metaGTx.processing documentation built on Oct. 2, 2022, 4:39 p.m.