Merge pull request #15 from ToonRosseel/fix_calling_bed

Fix calling bed
nf-cmgg · Jul 9, 2024 · 5fedc35 · 5fedc35
2 parents 36c111d + 5acc64d
commit 5fedc35
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Showing 3 changed files with 4 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -23,3 +23,5 @@ Initial release of nf-cmgg/exomecnv, created with the [nf-core](https://nf-co.re
 ### `Fixes`
 
 - Sort file of merged CNV calls to fix an issue with TABIX (needs sorted VCF files)
+- `CNV_CALL_X`: fix input channel to "roi_chrx"
+- allow sample numbers as sample names
diff --git a/bin/ExomeDepth_cnv_calling.R b/bin/ExomeDepth_cnv_calling.R
@@ -47,7 +47,7 @@ exons.GRanges <- GenomicRanges::GRanges(seqnames = exons$chromosome,
 
 # ### read counts ###
 cat("\nRead counting matrix\n")
-ExomeCount.dafr <- read.table(file=countfile,sep="\t",header = TRUE)
+ExomeCount.dafr <- read.table(file=countfile,sep="\t",header = TRUE,check.names = FALSE)
 # print(head(ExomeCount.dafr))
 # colnames(ExomeCount.dafr)
 

diff --git a/subworkflows/local/exomedepth/main.nf b/subworkflows/local/exomedepth/main.nf
@@ -127,7 +127,7 @@ workflow EXOMEDEPTH {
         .transpose(by:1)
 
     CNV_CALL_X(
-        ch_roi_auto, cnv_chrx_ch
+        ch_roi_x, cnv_chrx_ch
     )
 
     //MODULE: Group autosomal and chrX CNV per sample (one file for each sample)