Merge pull request #729 from maxulysse/dev_trailing_comma

fix issue with trailing commas
nf-core · Sep 5, 2022 · f1ab809 · f1ab809
2 parents 1f33d9b + b8b1aab
commit f1ab809
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -35,6 +35,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#706](https://github.com/nf-core/sarek/pull/706) - Fixed `vep_version` not found error when running `--vep_loftee`
 - [#724](https://github.com/nf-core/sarek/pull/724) - Fixed prettier issue
 - [#728](https://github.com/nf-core/sarek/pull/728) - Circumvent issue with controlfreec and length file containing regions not in intervals file
+- [#729](https://github.com/nf-core/sarek/pull/729) - Trailing commas in `--tools`, `--skip_tools` and `--use_gatk_spark` now raise failure cf [#722](https://github.com/nf-core/sarek/issues/722)
 
 ### Deprecated
 

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)*,?)*$"
+                    "pattern": "^((baserecalibrator|markduplicates)?,?)*[^,]+$"
                 }
             }
         },