From 9534c95d8a32e5f2de0ac5a4217470a29304d772 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 25 Mar 2024 11:36:34 +0100 Subject: [PATCH 1/2] change calls to casecalls --- subworkflows/local/variant_calling/call_sv_germlinecnvcaller.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/variant_calling/call_sv_germlinecnvcaller.nf b/subworkflows/local/variant_calling/call_sv_germlinecnvcaller.nf index a0636268..57ed2552 100644 --- a/subworkflows/local/variant_calling/call_sv_germlinecnvcaller.nf +++ b/subworkflows/local/variant_calling/call_sv_germlinecnvcaller.nf @@ -40,7 +40,7 @@ workflow CALL_SV_GERMLINECNVCALLER { GATK4_GERMLINECNVCALLER ( ch_gcnvc_in ) - GATK4_GERMLINECNVCALLER.out.calls.toList() + GATK4_GERMLINECNVCALLER.out.casecalls.toList() .flatMap {reduce_input(it)} .buffer (size: 2) .combine(ch_gcnvcaller_model.collect{it[1]}.toList()) From 21658fbc54c890935dfef7d6126c8798635020f9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 25 Mar 2024 12:31:54 +0100 Subject: [PATCH 2/2] update changelog and bump version --- CHANGELOG.md | 6 ++++++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 9 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f676b8d9..afabf4ad 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +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). +## 2.0.1 - Asterix (Patch) [2024-03-25] + +### `Fixed` + +- Germlinecnvcaller subworkflow uses the output channel `casecalls` from germlinecnvcaller module instead of `calls` which was invalid. [#535](https://github.com/nf-core/raredisease/issues/535) + ## 2.0.0 - Asterix [2024-03-18] ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index b3a8c6c8..1880cf3e 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -3,9 +3,9 @@ custom_logo_url: https://github.com/nf-core/raredisease/ custom_logo_title: "nf-core/raredisease" report_comment: > - This report has been generated by the nf-core/raredisease + This report has been generated by the nf-core/raredisease analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-raredisease-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index b3f5e3e2..2df0fde4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -293,7 +293,7 @@ manifest { description = """call and score variants from WGS/WES of rare disease patients""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.0.0' + version = '2.0.1' doi = '' }