Add deepsomatic tool

nf-core · Jan 9, 2025 · ba9109a · ba9109a
1 parent c29f7dc
commit ba9109a
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diff --git a/modules/nf-core/deepsomatic/environment.yml b/modules/nf-core/deepsomatic/environment.yml
diff --git a/modules/nf-core/deepsomatic/tests/main.nf.test.snap b/modules/nf-core/deepsomatic/tests/main.nf.test.snap
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -112,7 +112,7 @@
                     "fa_icon": "fas fa-toolbox",
                     "description": "Tools to use for duplicate marking, 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, GATK HaplotypeCaller, mpileup, Sentieon Haplotyper, Strelka\n- Structural Variants: indexcov, 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, Lofreq, 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), and bcftools annotate (needs `--bcftools_annotation`).\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|bcfann|cnvkit|controlfreec|deepvariant|deepsomatic|freebayes|haplotypecaller|lofreq|sentieon_dnascope|sentieon_haplotyper|manta|indexcov|merge|mpileup|msisensorpro|mutect2|ngscheckmate|sentieon_dedup|snpeff|strelka|tiddit|vep)?,?)*(?<!,)$"
+                    "pattern": "^((ascat|bcfann|cnvkit|controlfreec|deepvariant|deepsomatic|deepsomatic|freebayes|haplotypecaller|lofreq|sentieon_dnascope|sentieon_haplotyper|manta|indexcov|merge|mpileup|msisensorpro|mutect2|ngscheckmate|sentieon_dedup|snpeff|strelka|tiddit|vep)?,?)*(?<!,)$"
                 },
                 "skip_tools": {
                     "type": "string",