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fix issue with trailing commas #729

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Sep 5, 2022
Merged

fix issue with trailing commas #729

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b684170
fix issue with trailing commas
maxulysse Sep 5, 2022
b8b1aab
fix regex
maxulysse Sep 5, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -34,6 +34,7 @@ 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

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6 changes: 3 additions & 3 deletions nextflow_schema.json
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Expand Up @@ -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"
Expand Down Expand Up @@ -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)*,?)*$"
"pattern": "^((baserecalibrator|markduplicates)?,?)*[^,]+$"
}
}
},
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