script <- "
genome=$1
prefix=`basename $genome`
hisat2-build $genome $prefix
"
hisat2_index <- recipeMake(shscript = script,
paramID = c("genome"),
paramType = c("File"),
outputID = "htIdx",
outputGlob = "*.ht2*",
requireTools = "hisat2")
hisat2_index <- addMeta(
hisat2_index,
label = "hisat2_index",
doc = "HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. `hisat2-build` is used to build the index files.",
inputLabels = "reference genome",
inputDocs = "The reference genome file",
outputLabels = c("hisat2 index"),
outputDocs = c("A list of index files"),
extensions = list(
author = "rworkflow team",
date = Sys.Date(),
url = "http://daehwankimlab.github.io/hisat2/",
example = paste(
"hisat2_index.R <- recipeLoad('hisat2_index.R')",
"hisat2_index$genome <- 'GRCh38.primary_assembly.genome.fa'",
"getData(hisat2_index, outdir = 'data/folder', notes = c('hisat2_index', 'GRCh38.primary_assembly'))",
"",
"## Get data from local catch",
"dataUpdate('data/folder')",
"dataSearch(c('hisat2_index', 'GRCh38.primary_assembly'))",
"",
sep="\n"))
)
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