Merge branch 'master' into fusion_calling

.github/workflows/main.yml

@@ -45,7 +45,7 @@ jobs:
     - name: update apt
       run: sudo apt-get update
     - name: Free Disk Space (Ubuntu)
-      uses: jlumbroso/free-disk-space@v1.2.0
+      uses: jlumbroso/free-disk-space@v1.3.0
       with:
         # this might remove tools that are actually needed,
         # if set to "true" but frees about 6 GB
@@ -57,7 +57,7 @@ jobs:
         dotnet: true
         haskell: true
         large-packages: true
-        docker-images: true
+        docker-images: false
         swap-storage: true
 
     - uses: actions/checkout@v2

CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## [5.0.2](https://github.com/snakemake-workflows/dna-seq-varlociraptor/compare/v5.0.1...v5.0.2) (2023-10-09)
+
+
+### Bug Fixes
+
+* remove superfluous import of FTP remote provider ([ae68b90](https://github.com/snakemake-workflows/dna-seq-varlociraptor/commit/ae68b9079b92ddf6b0ace6888c171381d297ceee))
+
 ## [5.0.1](https://github.com/snakemake-workflows/dna-seq-varlociraptor/compare/v5.0.0...v5.0.1) (2023-08-25)
 
 

workflow/rules/candidate_calling.smk

@@ -19,8 +19,7 @@ rule freebayes:
         ),
     threads: max(workflow.cores - 1, 1)  # use all available cores -1 (because of the pipe) for calling
     wrapper:
-        #update to new release once available
-        "v2.6.0-35-g755343f/bio/freebayes"
+        "v2.7.0/bio/freebayes"
 
 
 rule delly:

workflow/rules/common.smk

@@ -3,11 +3,8 @@ from os import path
 
 import yaml
 import pandas as pd
-from snakemake.remote import FTP
 from snakemake.utils import validate
 
-ftp = FTP.RemoteProvider()
-
 validate(config, schema="../schemas/config.schema.yaml")
 
 samples = (

workflow/rules/qc.smk

@@ -48,4 +48,4 @@ rule multiqc:
     log:
         "logs/multiqc/{group}.log",
     wrapper:
-        "v2.3.2/bio/multiqc"
+        "v2.7.0/bio/multiqc"