script <- "
genome=$1
prefix=`basename $genome`
bowtie2-build $genome $prefix
"
bowtie2_index <- recipeMake(shscript = script,
paramID = c("genome"),
paramType = c("File"),
outputID = "btIdx",
outputGlob = "*.bt2",
requireTools = "bowtie2")
bowtie2_index <- addMeta(
bowtie2_index,
label = "bowtie2_index",
doc = "Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. `bowtie2-build` is used to build the index files.",
inputLabels = "reference genome",
inputDocs = "The reference genome file",
outputLabels = c("bowtie2 index"),
outputDocs = c("A list of bowtie index files"),
extensions = list(
author = "rworkflow team",
date = Sys.Date(),
url = "https://bowtie-bio.sourceforge.net/bowtie2/index.shtml",
example = paste(
"bowtie2_index <- recipeLoad('bowtie2_index')",
"bowtie2_index$genome <- 'GRCh38.primary_assembly.genome.fa' ## need to be a valid file path",
"getData(bowtie2_index, outdir = 'data/folder', notes = c('bowtie2_index', 'GRCh38.primary_assembly'))",
"",
"## Get data from local catch",
"dataUpdate('data/folder')",
"dataSearch(c('bowtie2_index', 'GRCh38'))",
"",
sep="\n"))
)
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