Merge pull request nf-core#1731 from maxulysse/controlfreec

Migrate controlfreec pytest to nf-test

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ 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

@@ -33,6 +33,7 @@ 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
 

modules.json

@@ -392,7 +392,7 @@
                     },
                     "samtools/mpileup": {
                         "branch": "master",
-                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "git_sha": "13e7d1046922381df90cd8fe9bee8c3e57ae8457",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {

modules/local/create_intervals_bed/main.nf

@@ -79,7 +79,7 @@ process CREATE_INTERVALS_BED {
     // def prefix_basename = prefix.substring(0, prefix.lastIndexOf("."))
 
     """
-    touch ${prefix}.bed
+    touch ${prefix}.stub.bed
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

tests/.nftignore

@@ -1,3 +1,4 @@
+.DS_Store
 annotation/**/*.vcf.{gz,gz.tbi}
 csv/*.csv
 multiqc/multiqc_data/gatk-base-recalibrator-reported-empirical-plot.txt
@@ -24,4 +25,4 @@ reports/snpeff/*/*_snpEff.csv
 reports/snpeff/*/snpEff_summary.html
 reports/vcftools/**/*.TsTv.qual
 variant_calling/**/*.vcf.{gz,gz.tbi}
-.DS_Store
+variant_calling/controlfreec/*/config.txt

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