script <- "
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/GRCh38.primary_assembly.genome.fa.gz
"
gencode_genome_grch38 <- recipeMake(script,
outputID = "genome",
outputGlob = "GRCh38.primary_assembly.genome.fa.gz")
gencode_genome_grch38 <- addMeta(
cwl = gencode_genome_grch38,
label = "gencode_genome_grch38",
doc = "Download human genome GRCh38 from GENCODE release 42",
outputLabels = c("genome"),
outputDocs = c("The `GRCh38.primary_assembly.genome.fa.gz` fasta file"),
extensions = list(
author = "rworkflow team",
url = "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/GRCh38.primary_assembly.genome.fa.gz",
date = Sys.Date(),
example = paste(
"Get data from evaluting recipe",
"gencode_genome_grch38 <- recipeLoad('gencode_genome_grch38')",
"getData(gencode_genome_grch38, outdir = 'data/folder', notes = c('gencode', 'genome', 'grch38', 'release 42'))",
"",
"## Get data from local catch",
"dataUpdate('data/folder')",
"dataSearch(c('gencode', 'genome', 'grch38', '42'))",
"",
"## Get data from Google bucket directly",
"dataUpdate('data/folder', cloud = TRUE)",
"dh <- dataSearch(c('gencode', 'genome', 'grch38'))",
"getCloudData(dh[dataNames(dh) == 'GRCh38.primary_assembly.genome.fa.gz'], outdir = 'data/folder')",
sep = "\n"))
)
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