From 8c452a8ff36fbb74e1902ae55583db068da7cd36 Mon Sep 17 00:00:00 2001 From: torossee Date: Mon, 8 Jul 2024 15:56:31 +0200 Subject: [PATCH 1/5] fix --- subworkflows/local/exomedepth/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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) From 6017b2388ac480a2cbc238b0283e38cc2c2ceb50 Mon Sep 17 00:00:00 2001 From: torossee Date: Mon, 8 Jul 2024 16:04:37 +0200 Subject: [PATCH 2/5] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1009252..7518a55 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,3 +23,4 @@ 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" From 5acc64deb7f03668d438f729ee462a58356f3df1 Mon Sep 17 00:00:00 2001 From: torossee Date: Mon, 8 Jul 2024 18:07:47 +0200 Subject: [PATCH 3/5] allow sample numbers as sample names --- CHANGELOG.md | 1 + bin/ExomeDepth_cnv_calling.R | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7518a55..dc81cad 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,3 +24,4 @@ Initial release of nf-cmgg/exomecnv, created with the [nf-core](https://nf-co.re - 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 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) From 8e8aceb39f1fa1e47b26c4389565000a289b42e7 Mon Sep 17 00:00:00 2001 From: torossee Date: Wed, 10 Jul 2024 12:57:21 +0200 Subject: [PATCH 4/5] bump to 1.0.2 --- CHANGELOG.md | 20 ++++++++++++-------- assets/multiqc_config.yml | 2 +- nextflow.config | 2 +- 3 files changed, 14 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index dc81cad..6bfd1ff 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,14 +2,12 @@ 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). +## v1.0.2 - Youthful Yamal [2024-07-10] -## 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` +### `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] @@ -23,5 +21,11 @@ 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) -- `CNV_CALL_X`: fix input channel to "roi_chrx" -- allow sample numbers as sample names + +## 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/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 = '' } From f654f8cd79e7d341c178bcb4a6f5e46f476a77e6 Mon Sep 17 00:00:00 2001 From: torossee Date: Wed, 10 Jul 2024 13:02:35 +0200 Subject: [PATCH 5/5] prettier --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6bfd1ff..619dcca 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,7 @@ 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). + ## v1.0.2 - Youthful Yamal [2024-07-10] ### `Fixes`