From 82f563dd0bca8b8c0c9f2a7197e73d18d6dc5130 Mon Sep 17 00:00:00 2001 From: Rike Date: Mon, 15 Aug 2022 21:05:43 +0200 Subject: [PATCH 1/4] freec ploidy number -> String --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 20063bdc6b..940196d41c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -316,7 +316,7 @@ "help_text": "Details, see [ControlFREEC manual](http://boevalab.inf.ethz.ch/FREEC/tutorial.html)." }, "cf_ploidy": { - "type": "integer", + "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).", From 23103b540db39c2ad519f31c9f99be42976fe163 Mon Sep 17 00:00:00 2001 From: Rike Date: Mon, 15 Aug 2022 21:08:22 +0200 Subject: [PATCH 2/4] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 688ff2b520..82afb5d6c4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 From baa917fe878ac4f24fafcf13954835ac526104d0 Mon Sep 17 00:00:00 2001 From: Rike Date: Mon, 15 Aug 2022 21:19:02 +0200 Subject: [PATCH 3/4] also update config --- nextflow.config | 2 +- nextflow_schema.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index f4dd8157af..54b78ec60d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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 diff --git a/nextflow_schema.json b/nextflow_schema.json index 940196d41c..c31fe317af 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -317,7 +317,7 @@ }, "cf_ploidy": { "type": "string", - "default": 2, + "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", From ce4b0a83034211fcb0445e5571e742643e448d3a Mon Sep 17 00:00:00 2001 From: Rike Date: Mon, 15 Aug 2022 21:26:52 +0200 Subject: [PATCH 4/4] unfortuantely also needs to be ignored by validation --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 54b78ec60d..c1fca80120 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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