Merge pull request #536 from nf-core/patch

Patch release 2.0.1

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`

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 <a href="https://github.com/nf-core/raredisease/releases/tag/2.0.0" target="_blank">nf-core/raredisease</a>
+  This report has been generated by the <a href="https://github.com/nf-core/raredisease/releases/tag/2.0.1" target="_blank">nf-core/raredisease</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/raredisease/2.0.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/raredisease/2.0.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-raredisease-methods-description":
     order: -1000

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             = ''
 }
 

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())