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Change platform description and update vcf2cytosure conditional #607

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Sep 11, 2024
Merged

Change platform description and update vcf2cytosure conditional #607

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9 changes: 4 additions & 5 deletions nextflow_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -485,9 +485,9 @@
"analysis_type": {
"type": "string",
"default": "wgs",
"description": "Specifies which analysis type for the pipeline- either 'wgs','wes','mito'. This changes resources consumed and tools used.",
"description": "Specifies which analysis type for the pipeline- either 'wgs' or 'wes'. This changes resources consumed and tools used.",
"fa_icon": "fas fa-align-center",
"enum": ["wgs", "wes", "mito"]
"enum": ["wgs", "wes"]
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Good catch!

},
"bwa_as_fallback": {
"type": "boolean",
Expand All @@ -498,9 +498,8 @@
"platform": {
"type": "string",
"default": "illumina",
"description": "Specifies which analysis type for the pipeline- either 'wgs','wes','mito'. This changes resources consumed and tools used.",
"fa_icon": "fas fa-align-center",
"enum": ["illumina"]
"description": "Specifies the platform on which the reads were sequenced.",
"fa_icon": "fas fa-align-center"
},
"ngsbits_samplegender_method": {
"type": "string",
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2 changes: 1 addition & 1 deletion workflows/raredisease.nf
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Expand Up @@ -785,7 +785,7 @@ workflow RAREDISEASE {
Generate CGH files from sequencing data
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
if ( !params.skip_vcf2cytosure && params.analysis_type.equals("wgs") && !params.skip_sv_calling) {
if ( !params.skip_vcf2cytosure && params.analysis_type.equals("wgs") && !params.skip_sv_calling && !params.skip_sv_annotation) {
GENERATE_CYTOSURE_FILES (
ch_sv_annotate.vcf_ann,
ch_sv_annotate.tbi,
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