bpipe_rna_mouse.pipeline

//file containing Bpipe call for MOUSE RNA expression pipeline


// LOAD STAGES
load 'bpipe_dna.stages'
load 'bpipe_rna.stages'

// LOAD CONFIG
load 'bpipe_rna_mouse.config'


Bpipe.run {
	getVersions +
	"%_R*.fastq" * [ qc ] +
	"%_R*.fastq" * [ alignSTAR + indexPIC + dedupOptPIC ] +
        "%.dedupOptPIC.bam" * [ idxstatPIC, countHTSeq_unstranded, countHTSeq_sameStranded, countHTSeq_otherStranded ] +
        cleanUp
}