Migrate controlfreec pytest to nf-test

.github/workflows/ci.yml

@@ -12,7 +12,7 @@ on:
 env:
   NFT_DIFF: "pdiff"
   NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
-  NFT_VER: "0.9.0"
+  NFT_VER: "0.9.2"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity

CHANGELOG.md

@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1707](https://github.com/nf-core/sarek/pull/1707) - Un-hide parameters and clean up Json schema
 - [1708](https://github.com/nf-core/sarek/pull/1708) - Migrate pipeline pytest alignment and annotation tests to nf-test
 - [1711](https://github.com/nf-core/sarek/pull/1711) - Migrate pipeline pytest strelka tests to nf-test
+- [1731](https://github.com/nf-core/sarek/pull/1731) - Migrate pipeline pytest controlfreec tests to nf-test
 
 ### Fixed
 

tests/config/pytesttags.yml

@@ -96,27 +96,6 @@ cnvkit:
   - tests/csv/3.0/recalibrated_tumoronly.csv
   - tests/test_cnvkit.yml
 
-## controlfreec
-controlfreec:
-  - conf/modules/controlfreec.config
-  - conf/modules/mpileup.config
-  - modules/nf-core/cat/cat/**
-  - modules/nf-core/controlfreec/assesssignificance/**
-  - modules/nf-core/controlfreec/freec/**
-  - modules/nf-core/controlfreec/freec2bed/**
-  - modules/nf-core/controlfreec/freec2circos/**
-  - modules/nf-core/controlfreec/makegraph2/**
-  - modules/nf-core/mosdepth/**
-  - modules/nf-core/samtools/mpileup/**
-  - subworkflows/local/bam_variant_calling_mpileup/**
-  - subworkflows/local/bam_variant_calling_somatic_all/**
-  - subworkflows/local/bam_variant_calling_somatic_controlfreec/**
-  - subworkflows/local/bam_variant_calling_tumor_only_all/**
-  - subworkflows/local/bam_variant_calling_tumor_only_controlfreec/**
-  - tests/csv/3.0/recalibrated_somatic.csv
-  - tests/csv/3.0/recalibrated_tumoronly.csv
-  - tests/test_controlfreec.yml
-
 ## deepvariant
 deepvariant:
   - conf/modules/deepvariant.config