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Commit cde5c10a authored by Venkat Malladi's avatar Venkat Malladi
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fix missing genome params and annotate peaks syntax.

parent 78b410c7
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1 merge request!18Resolve "Add in current chip-analysis functionality."
...@@ -38,6 +38,7 @@ readsList = Channel ...@@ -38,6 +38,7 @@ readsList = Channel
pairedEnd = params.pairedEnd pairedEnd = params.pairedEnd
designFile = params.designFile designFile = params.designFile
genomeSize = params.genomeSize genomeSize = params.genomeSize
genome = params.genome
chromSizes = params.chromSizes chromSizes = params.chromSizes
fasta = params.fasta fasta = params.fasta
cutoffRatio = params.cutoffRatio cutoffRatio = params.cutoffRatio
......
...@@ -21,16 +21,16 @@ if (length(args) != 2) { ...@@ -21,16 +21,16 @@ if (length(args) != 2) {
} }
design_file <- args[1] design_file <- args[1]
genome <-args[2] genome_assembly <- args[2]
# Load UCSC Known Genes # Load UCSC Known Genes
if(genome=='GRCh37') { if(genome_assembly=='GRCh37') {
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
annodb <- 'org.Hs.eg.db' annodb <- 'org.Hs.eg.db'
} else if(genome=='GRCm38') { } else if(genome_assembly=='GRCm38') {
txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
annodb <- 'org.Mm.eg.db' annodb <- 'org.Mm.eg.db'
} else if(genome=='GRCh38') { } else if(genome_assembly=='GRCh38') {
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
annodb <- 'org.Hs.eg.db' annodb <- 'org.Hs.eg.db'
} }
......
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