Merge pull request #16 from nf-cmgg/dev

fix_calling_bed branch into master
nf-cmgg · Jul 10, 2024 · c9179d8 · c9179d8
2 parents 3c717db + b3ed555
commit c9179d8
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diff --git 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
@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-cmgg/exomecnv/releases/tag/1.0.1" target="_blank">nf-cmgg/exomecnv</a>
+  This report has been generated by the <a href="https://github.com/nf-cmgg/exomecnv/releases/tag/1.0.2" target="_blank">nf-cmgg/exomecnv</a>
   analysis pipeline.
 report_section_order:
   "nf-cmgg-exomecnv-methods-description":

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/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
@@ -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)