fix regex

nf-core · Sep 5, 2022 · b8b1aab · b8b1aab
1 parent b684170
commit b8b1aab
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -89,14 +89,14 @@
                     "fa_icon": "fas fa-toolbox",
                     "description": "Tools to use for variant calling and/or for annotation.",
                     "help_text": "Multiple tools separated with commas.\n\n**Variant Calling:**\n\nGermline variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: DeepVariant, FreeBayes, HaplotypeCaller, mpileup, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit\n\nTumor-only somatic variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, mpileup, Mutect2, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit, ControlFREEC\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, Mutect2, Strelka2\n- Structural variants: Manta, TIDDIT\n- Copy-Number: ASCAT, CNVKit, Control-FREEC\n- Microsatellite Instability: MSIsensorpro\n\n> **NB** Mutect2 for somatic variant calling cannot be combined with `--no_intervals`\n\n**Annotation:**\n \n- snpEff, VEP, merge (both consecutively).\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted when starting from `--step annotate`.",
-                    "pattern": "^((ascat|cnvkit|controlfreec|deepvariant|freebayes|haplotypecaller|manta|merge|mpileup|msisensorpro|mutect2|snpeff|strelka|tiddit|vep)*,?)*[^,]$"
+                    "pattern": "^((ascat|cnvkit|controlfreec|deepvariant|freebayes|haplotypecaller|manta|merge|mpileup|msisensorpro|mutect2|snpeff|strelka|tiddit|vep)?,?)*[^,]+$"
                 },
                 "skip_tools": {
                     "type": "string",
                     "fa_icon": "fas fa-forward",
                     "description": "Disable specified tools.",
                     "help_text": "Multiple tools can be specified, separated by commas.\n\n> **NB** `--skip_tools baserecalibrator_report` is actually just not saving the reports.\n> **NB** `--skip_tools markduplicates_report` does not skip `MarkDuplicates` but prevent the collection of duplicate metrics that slows down performance.",
-                    "pattern": "^((baserecalibrator|baserecalibrator_report|bcftools|documentation|fastqc|markduplicates|markduplicates_report|mosdepth|multiqc|samtools|vcftools|versions)*,?)*[^,]$"
+                    "pattern": "^((baserecalibrator|baserecalibrator_report|bcftools|documentation|fastqc|markduplicates|markduplicates_report|mosdepth|multiqc|samtools|vcftools|versions)?,?)*[^,]+$"
                 }
             },
             "fa_icon": "fas fa-user-cog"
@@ -215,7 +215,7 @@
                     "fa_icon": "fas fa-forward",
                     "description": "Enable usage of GATK Spark implementation for duplicate marking and/or base quality score recalibration",
                     "help_text": "Multiple separated with commas.\n\n> The GATK4 Base Quality Score recalibration tools `Baserecalibrator` and `ApplyBQSR` are currently available as Beta release. Use with caution!",
-                    "pattern": "^((baserecalibrator|markduplicates)*,?)*[^,]$"
+                    "pattern": "^((baserecalibrator|markduplicates)?,?)*[^,]+$"
                 }
             }
         },