feat: added cnvyptor to varcall_py3 container (#991)

* added cnvyptor

* update changelog

BALSAMIC/containers/varcall_py3/varcall_py3.yaml

@@ -14,5 +14,6 @@ dependencies:
   - bioconda::vcfpy=0.13.4
   - bioconda::bwa=0.7.17
   - bioconda::tiddit=3.3.0
+  - bioconda::cnvpytor=1.2.1
   - conda-forge::libiconv
   - conda-forge::r-base=4.1.1

CHANGELOG.rst

@@ -6,6 +6,8 @@ Added:
 
 * Use of PON reference, if exists for CNVkit tumor-normal analysis https://github.com/Clinical-Genomics/BALSAMIC/pull/982
 * Added PON version to CLI and config.json https://github.com/Clinical-Genomics/BALSAMIC/pull/983
+* `cnvpytor` to varcallpy3 container https://github.com/Clinical-Genomics/BALSAMIC/pull/991
+
 
 Changed:
 ^^^^^^^^

container_tests/varcall_py3/varcall_py3.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 # Test if commands exist
 
-valid_commands=( "bcftools" "samtools" "tabix" "vardict" "vardict-java" "svdb" "bwa" "tiddit")
+valid_commands=( "bcftools" "samtools" "tabix" "vardict" "vardict-java" "svdb" "bwa" "tiddit" "cnvpytor")
 
 for valid_command in "${valid_commands[@]}"
 do