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remove cf len file from config #841

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merged 3 commits into from
Nov 15, 2022
Merged

remove cf len file from config #841

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a7de376
remove cf len file from config to avoid precedence issues
FriederikeHanssen Nov 15, 2022
e9071d6
changelog
FriederikeHanssen Nov 15, 2022
c9674a8
Merge branch 'dev' into cf
FriederikeHanssen Nov 15, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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

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1 change: 0 additions & 1 deletion nextflow.config
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Expand Up @@ -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
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