script <- "
filename=$1
idx=$2
url=https://storage.googleapis.com/gatk-best-practices/somatic-hg38/$filename
wget $url
if [[ $idx ]]; then wget $url.$idx; fi
"
gcp_gatk_mutect2_hg38 <- recipeMake(shscript = script,
paramID = c("filename", "idx"),
paramType = c("string", "string?"),
outputID = "gfile",
outputGlob = "$(inputs.filename)*")
gcp_gatk_mutect2_hg38 <- addMeta(
gcp_gatk_mutect2_hg38,
label = "gcp_gatk_mutect2_hg38",
doc = "GATK mutect2 bundle for hg38 from GCP (gs://gatk-best-practices/somatic-hg38)",
inputLabels = c("file name", "index"),
inputDocs = c("The file basename to download from the broad GCP bucket",
"The 'idx' or 'tbi' index file if existing"),
outputLabels = c("gfile"),
outputDocs = c("The downloaded annotation files"),
extensions = list(
author = "rworkflow team",
date = Sys.Date(),
url = "https://console.cloud.google.com/storage/browser/gatk-best-practices/somatic-hg38",
example = paste(
"gcp_gatk_mutect2_hg38 <- recipeLoad('gcp_gatk_mutect2_hg38')",
"gcp_gatk_mutect2_hg38$filename <- 'small_exac_common_3.hg38.vcf.gz'",
"gcp_gatk_mutect2_hg38$idx <- 'tbi'",
"getData(gcp_gatk_mutect2_hg38, outdir = 'data/folder', notes = c('gcp', 'gatk', 'mutect2', 'hg38', 'small_exac_common'))",
"",
"## Get data from local catch",
"dataUpdate('data/folder')",
"dataSearch(c('gcp', 'gatk', 'hg38'))",
"",
sep="\n"))
)
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