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Commit 8ae1644d authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Try and fix CI countData

parent cede66a7
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2 merge requests!58Develop,!53Resolve "process_derivaUpload"
Pipeline #8553 canceled with stages
...@@ -7,7 +7,7 @@ option_list=list( ...@@ -7,7 +7,7 @@ option_list=list(
opt=parse_args(OptionParser(option_list=option_list)) opt=parse_args(OptionParser(option_list=option_list))
rm(option_list) rm(option_list)
countTable <- read.csv(paste0(opt$repRID,"_countTable.csv"), stringsAsFactors=FALSE) countTable <- read.csv(paste0(opt$repRID,".countTable.csv"), stringsAsFactors=FALSE)
geneID <- read.delim("geneID.tsv", header=FALSE, stringsAsFactors=FALSE) geneID <- read.delim("geneID.tsv", header=FALSE, stringsAsFactors=FALSE)
Entrez <- read.delim("Entrez.tsv", header=FALSE, stringsAsFactors=FALSE) Entrez <- read.delim("Entrez.tsv", header=FALSE, stringsAsFactors=FALSE)
...@@ -23,4 +23,4 @@ output <- merge(x=convert,y=countTable[,c("gene_name","gene_id","count","tpm")], ...@@ -23,4 +23,4 @@ output <- merge(x=convert,y=countTable[,c("gene_name","gene_id","count","tpm")],
colnames(output) <- c("GENCODE_Gene_Symbol","NCBI_GeneID","Ensembl_GeneID","count","tpm") colnames(output) <- c("GENCODE_Gene_Symbol","NCBI_GeneID","Ensembl_GeneID","count","tpm")
output <- output[,c(1,3,2,4:5)] output <- output[,c(1,3,2,4:5)]
write.table(output,file=paste0(opt$repRID,".tpmTable.csv"),sep=",",row.names=FALSE,quote=FALSE) write.table(output,file=paste0(opt$repRID,"_tpmTable.csv"),sep=",",row.names=FALSE,quote=FALSE)
...@@ -16,4 +16,4 @@ def test_makeFeatureCounts(): ...@@ -16,4 +16,4 @@ def test_makeFeatureCounts():
assert os.path.exists(os.path.join( assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se.countTable.csv')) data_output_path, 'Q-Y5F6_1M.se.countTable.csv'))
assert os.path.exists(os.path.join( assert os.path.exists(os.path.join(
data_output_path, 'Q-Y5F6_1M.se.tpmTable.csv')) data_output_path, 'Q-Y5F6_1M.se_tpmTable.csv'))
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