Fix parameter for GATK HC too

Author: jfy133

conf/modules.config

@@ -1648,8 +1648,7 @@ process {
         tag        = { "${meta.reference}|${meta.sample_id}" }
         ext.args   = {
             [
-                "--sample-ploidy ${meta2.ploidy}",
-                ref_meta.ploidy ? "--sample-ploidy ${ref_meta.ploidy}" : "--sample-ploidy 2",
+                meta2.ploidy ? "--sample_ploidy ${meta2.ploidy}" : "--sample_ploidy 2",
                 "-stand-call-conf ${params.genotyping_gatk_call_conf}",
                 "--output-mode ${params.genotyping_gatk_hc_out_mode}",
                 "--emit-ref-confidence ${params.genotyping_gatk_hc_emitrefconf}",

nextflow_schema.json

@@ -1088,7 +1088,7 @@
                     "type": "integer",
                     "default": 2,
                     "description": "Specify the ploidy of the reference organism.",
-                    "help_text": "Specify the desired ploidy value of your reference organism for genotyping with GATK or FreeBayes. E.g. if you want to allow heterozygous calls this value should be >= 2.\n\n> Modifies GATK UnifiedGenotyper parameter: `--sample_ploidy`\n> Modifies GATK HaplotypeCaller parameter: `--sample-ploidy`\n> Modifies FreeBayes parameter: `-p`",
+                    "help_text": "Specify the desired ploidy value of your reference organism for genotyping with GATK or FreeBayes. E.g. if you want to allow heterozygous calls this value should be >= 2.\n\n> Modifies GATK UnifiedGenotyper parameter: `--sample_ploidy`\n> Modifies GATK HaplotypeCaller parameter: `--sample_ploidy`\n> Modifies FreeBayes parameter: `-p`",
                     "fa_icon": "fas fa-pastafarianism"
                 },
                 "genotyping_pileupcaller_min_base_quality": {