Fix problems with illegal R column names

nf-core · Nov 19, 2023 · 6a64bd8 · 6a64bd8
1 parent 6b87b61
commit 6a64bd8
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Showing 2 changed files with 1 addition and 3 deletions.
diff --git a/bin/reformat_count_matrix.R b/bin/reformat_count_matrix.R
@@ -4,7 +4,7 @@
 ## License: MIT
 
 library(dplyr)
-mat <- read.table("circRNA_matrix.txt", sep="\t", header=T, stringsAsFactors=F)
+mat <- read.table("circRNA_matrix.txt", sep="\t", header=T, stringsAsFactors=F, check.names=F)
 mat$ID <- with(mat, paste0(Chr, sep=":", Start, sep="-", Stop, sep=":", Strand))
 mat <- mat[,-c(1:4)]
 mat1 <- mat %>% select(ID, everything())

diff --git a/modules/local/count_matrix/combined/main.nf b/modules/local/count_matrix/combined/main.nf
@@ -31,9 +31,7 @@ process COUNTS_COMBINED {
     "${task.process}":
         awk: \$(awk --version | head -n 1 | cut -d' ' -f3 | sed 's/,//g')
         r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
-        argparser: \$(Rscript -e "library(arparser); cat(as.character(packageVersion('argparser')))")
         dplyr: \$(Rscript -e "library(dplyr); cat(as.character(packageVersion('dplyr')))")
-        python: \$(python --version | sed -e 's/Python //g')
     END_VERSIONS
     """
 }