diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1009252..619dcca 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,13 +3,12 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-## v1.0.0 - Dashing Doku - [2024-06-12]
-
-Initial release of nf-cmgg/exomecnv, created with the [nf-core](https://nf-co.re/) template v2.13.
+## v1.0.2 - Youthful Yamal [2024-07-10]
-### `Added`
+### `Fixes`
-- First release of the pipeline - CNV calling using [ExomeDepth](https://github.com/vplagnol/ExomeDepth)
+- `CNV_CALL_X`: fix input channel to "roi_chrx"
+- allow sample numbers as sample names
## v1.0.1 - Lightning Lukaku [2024-06-19]
@@ -23,3 +22,11 @@ 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)
+
+## v1.0.0 - Dashing Doku - [2024-06-12]
+
+Initial release of nf-cmgg/exomecnv, created with the [nf-core](https://nf-co.re/) template v2.13.
+
+### `Added`
+
+- First release of the pipeline - CNV calling using [ExomeDepth](https://github.com/vplagnol/ExomeDepth)
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 0135229..c33e7c2 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
report_comment: >
- This report has been generated by the nf-cmgg/exomecnv
+ This report has been generated by the nf-cmgg/exomecnv
analysis pipeline.
report_section_order:
"nf-cmgg-exomecnv-methods-description":
diff --git a/bin/ExomeDepth_cnv_calling.R b/bin/ExomeDepth_cnv_calling.R
index 216bdb0..02529d1 100755
--- 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/nextflow.config b/nextflow.config
index 5d5635f..fa5f64d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -249,7 +249,7 @@ manifest {
description = """A nextflow pipeline for calling exome CNVs"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
- version = '1.0.1'
+ version = '1.0.2'
doi = ''
}
diff --git a/subworkflows/local/exomedepth/main.nf b/subworkflows/local/exomedepth/main.nf
index cfebd74..423e183 100644
--- 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)