yq_merge_cmd: Merge two YAML files using the 'yq' tool.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Merge two YAML files using the yq tool.

Description

Merge two YAML files using the yq tool.

Usage

yq_merge_cmd(
  f1,
  f2,
  stdout = TRUE,
  check_yq = TRUE,
  check_exit = TRUE,
  yq_binary = getOption("scdrake_yq_binary")
)

Arguments

f1, f2	A character scalar: path to YAML file. f2 is the file whose parameters will overwrite those in f1.
stdout	A character or logical scalar, or NULL: passed to base::system2(). For character scalar: path to file into which the resulting merged YAML file will be written. If empty string (""), the result will be written to R console. For logical scalar TRUE: return the stdout as a character scalar. For logical scalar FALSE, or NULL: discard the stdout.
check_yq	A logical scalar: if TRUE, check yq tool presence with check_yq() prior to merging.
check_exit	A logical scalar: if TRUE and stdout is FALSE, check exit code of shell command used for merging.
yq_binary	A character scalar: path to yq tool's binary.

Value

An output from base::system2() - depends on the stdout argument.

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.