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freec ploidy number -> String #704

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merged 4 commits into from
Aug 16, 2022
Merged

freec ploidy number -> String #704

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82f563d
freec ploidy number -> String
FriederikeHanssen Aug 15, 2022
23103b5
update changelog
FriederikeHanssen Aug 15, 2022
baa917f
also update config
FriederikeHanssen Aug 15, 2022
ce4b0a8
unfortuantely also needs to be ignored by validation
FriederikeHanssen Aug 15, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#681](https://github.com/nf-core/sarek/pull/681) - Fixed intermediate files published cf [#680](https://github.com/nf-core/sarek/issues/680)
- [#688](https://github.com/nf-core/sarek/pull/688) - Fixed VEP plugins issue cf [#687](https://github.com/nf-core/sarek/issues/687)
- [#689](https://github.com/nf-core/sarek/pull/689) - Fixed when clause for non `BWA mem` building mapping indexes
- [#704](https://github.com/nf-core/sarek/pull/704) - Fixed `cf_ploidy` to string instead of number

### Deprecated

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4 changes: 2 additions & 2 deletions nextflow.config
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Expand Up @@ -55,7 +55,7 @@ params {
ascat_min_counts = 10 // default value for ASCAT
ascat_min_map_qual = 35 // default value for ASCAT
ascat_purity = null // default value for ASCAT
cf_ploidy = 2 // default value for Control-FREEC
cf_ploidy = "2" // default value for Control-FREEC
cf_coeff = 0.05 // default value for Control-FREEC
cf_contamination = 0 // default value for Control-FREEC
cf_contamination_adjustment = false // by default we are not using this in Control-FREEC
Expand Down Expand Up @@ -101,7 +101,7 @@ params {
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,snpeff_version,vep_version'
schema_ignore_params = 'genomes,snpeff_version,vep_version,cf_ploidy'
enable_conda = false

// Config options
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4 changes: 2 additions & 2 deletions nextflow_schema.json
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Expand Up @@ -316,8 +316,8 @@
"help_text": "Details, see [ControlFREEC manual](http://boevalab.inf.ethz.ch/FREEC/tutorial.html)."
},
"cf_ploidy": {
"type": "integer",
"default": 2,
"type": "string",
"default": "2",
"fa_icon": "fas fa-bacon",
"help_text": "In case of doubt, you can set different values and Control-FREEC will select the one that explains most observed CNAs Example: ploidy=2 , ploidy=2,3,4. For more details, see the [manual](http://boevalab.inf.ethz.ch/FREEC/tutorial.html).",
"description": "Genome ploidy used by ControlFREEC",
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