From a7de3765f351e9b65c7a9ac5e6f5796095ede363 Mon Sep 17 00:00:00 2001 From: Rike Date: Tue, 15 Nov 2022 13:19:11 +0100 Subject: [PATCH 1/2] remove cf len file from config to avoid precedence issues --- nextflow.config | 1 - 1 file changed, 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index bf074101ca..ca9baa35ad 100644 --- a/nextflow.config +++ b/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 From e9071d6e02a54bad7bf3688ebde14fd7335baebd Mon Sep 17 00:00:00 2001 From: Rike Date: Tue, 15 Nov 2022 14:12:20 +0100 Subject: [PATCH 2/2] changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index aee6544440..5e3ca98535 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -46,6 +46,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#814](https://github.com/nf-core/sarek/pull/814) - Fix readgroups when using DragMap together with FreeBayes or Mutect2 (see issue [#780](https://github.com/nf-core/sarek/issues/780)) - [#817](https://github.com/nf-core/sarek/pull/817) - Fix CNVKit run on tumor-only sample to be run on all samples - [#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 +- [#841](https://github.com/nf-core/sarek/pull/841) - Fix path priority for `cf_chrom_len` ### Deprecated