Merge pull request #841 from FriederikeHanssen/cf

remove cf len file from config

CHANGELOG.md

@@ -49,6 +49,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#828](https://github.com/nf-core/sarek/pull/817) - Fix issue [#763](https://github.com/nf-core/sarek/issues/763) to run variantcalling when starting form step recalibration
 - [#837](https://github.com/nf-core/sarek/pull/837) - Fix Freebayes config selector after subworkflow renaming
 - [#839](https://github.com/nf-core/sarek/pull/839) - Remove `copyTo` method that fails on S3 when the source and destination buckets are in different regions
+- [#841](https://github.com/nf-core/sarek/pull/841) - Fix path priority for `cf_chrom_len`
 
 ### Deprecated
 

nextflow.config

@@ -62,7 +62,6 @@ params {
     cf_mincov                   = 0     // ControlFreec default values
     cf_minqual                  = 0     // ControlFreec default values
     cf_window                   = null  // by default we are not using this in Control-FREEC
-    cf_chrom_len                = null  // by default we are using the fasta_fai. This can be used to circumvent this issue until there is a better option available upstream: https://github.com/nf-core/sarek/issues/670
     cnvkit_reference            = null  // by default the reference is build from the fasta file
     ignore_soft_clipped_bases   = false // no --dont-use-soft-clipped-bases for GATK Mutect2
     wes                         = false // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers