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Fix calling bed #15

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merged 4 commits into from
Jul 9, 2024
Merged

Fix calling bed #15

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3c717db
Merge pull request #14 from nf-cmgg/dev
ToonRosseel Jul 2, 2024
8c452a8
fix
ToonRosseel Jul 8, 2024
6017b23
update changelog
ToonRosseel Jul 8, 2024
5acc64d
allow sample numbers as sample names
ToonRosseel Jul 8, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -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
2 changes: 1 addition & 1 deletion bin/ExomeDepth_cnv_calling.R
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Expand Up @@ -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)

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2 changes: 1 addition & 1 deletion subworkflows/local/exomedepth/main.nf
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Expand Up @@ -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)
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