Auto-generate templates for Snakemake rules and R scripts
autosmk auto generates templates given a list of input and output files for a Snakemake rule passing the inputs/outputs to an R script. For example, if we specify
inputs <- c(
'important_csv' = 'data/input_{id}.csv',
'compressed_R_object' = 'data/input_{id}.rds'
)
outputs <- c(
'figure' = 'figs/fig_{id}.png'
)as rules for some files and call
dir <- tempdir()
autosmk('testrule',
inputs,
outputs,
dir,
open = FALSE)then we can generate a template for a Snakemake rule like
rule testrule:
input:
important_csv="data/input_{id}.csv",
compressed_R_object="data/input_{id}.rds"
output:
figure="figs/fig_{id}.png"
shell:
"""
Rscript testrule.R \
--important_csv {input.important_csv} \
--compressed_R_object {input.compressed_R_object} \
--figure {output.figure}
"""with the R script to be called
library(aargh)
testrule <- function(important_csv = "str",
compressed_R_object = "str",
figure = "str") {
}
aargh(testrule)