Merge pull request #1536 from maxulysse/dev

Fix typo (strelka2 -> strelka)
nf-core · May 27, 2024 · f2852ff · f2852ff
2 parents 76367cc + 7d6a0d6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- [#1536](https://github.com/nf-core/sarek/pull/1536) - Correct typo `Strelka2` to `Strelka`
 - [#1541](https://github.com/nf-core/sarek/pull/1541) - Getting bam and bai published in the same folder
 - [#1542](https://github.com/nf-core/sarek/pull/1542) - Removing legacy configs of `CUSTOM_DUMPSOFTWAREVERSIONS`
 

diff --git a/docs/output.md b/docs/output.md
@@ -41,7 +41,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
       - [Sentieon DNAscope joint germline variant calling](#sentieon-dnascope-joint-germline-variant-calling)
     - [Sentieon Haplotyper](#sentieon-haplotyper)
       - [Sentieon Haplotyper joint germline variant calling](#sentieon-haplotyper-joint-germline-variant-calling)
-    - [Strelka2](#strelka2)
+    - [Strelka](#strelka)
   - [Structural Variants](#structural-variants)
     - [Manta](#manta)
     - [TIDDIT](#tiddit)
@@ -542,9 +542,9 @@ In Sentieon's package DNAseq, joint germline variant calling is done by first ru
 
 </details>
 
-#### Strelka2
+#### Strelka
 
-[Strelka2](https://github.com/Illumina/strelka) is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. For further reading and documentation see the [Strelka2 user guide](https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md). If [Strelka2](https://github.com/Illumina/strelka) is used for somatic variant calling and [Manta](https://github.com/Illumina/manta) is also specified in tools, the output candidate indels from [Manta](https://github.com/Illumina/manta) are used according to [Strelka Best Practices](https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic-configuration-example).
+[Strelka](https://github.com/Illumina/strelka) is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. For further reading and documentation see the [Strelka user guide](https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md). If [Strelka](https://github.com/Illumina/strelka) is used for somatic variant calling and [Manta](https://github.com/Illumina/manta) is also specified in tools, the output candidate indels from [Manta](https://github.com/Illumina/manta) are used according to [Strelka Best Practices](https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic-configuration-example).
 For further downstream analysis, take a look [here](https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#interpreting-the-germline-multi-sample-variants-vcf).
 
 <details markdown="1">
@@ -576,7 +576,7 @@ For further downstream analysis, take a look [here](https://github.com/Illumina/
 
 [Manta](https://github.com/Illumina/manta) calls structural variants (SVs) and indels from mapped paired-end sequencing reads.
 It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
-[Manta](https://github.com/Illumina/manta) provides a candidate list for small indels that can be fed to [Strelka2](https://github.com/Illumina/strelka) following [Strelka Best Practices](https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic-configuration-example). For further reading and documentation see the [Manta user guide](https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md).
+[Manta](https://github.com/Illumina/manta) provides a candidate list for small indels that can be fed to [Strelka](https://github.com/Illumina/strelka) following [Strelka Best Practices](https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic-configuration-example). For further reading and documentation see the [Manta user guide](https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md).
 
 <details markdown="1">
 <summary>Output files for normal samples</summary>
@@ -823,7 +823,7 @@ It requires a normal sample for each tumour to differentiate the somatic and ger
 
 ### Concatenation
 
-Germline VCFs from `DeepVariant`, `FreeBayes`, `HaplotypeCaller`, `Haplotyper`, `Manta`, `bcftools mpileup`, `Strelka2`, or `Tiddit` are concatenated with `bcftools concat`. The field `SOURCE` is added to the VCF header to report the variant caller.
+Germline VCFs from `DeepVariant`, `FreeBayes`, `HaplotypeCaller`, `Haplotyper`, `Manta`, `bcftools mpileup`, `Strelka`, or `Tiddit` are concatenated with `bcftools concat`. The field `SOURCE` is added to the VCF header to report the variant caller.
 
 <details markdown="1">
 <summary>Concatenated VCF-files for normal samples</summary>
@@ -1067,7 +1067,7 @@ For further reading and documentation see the [bcftools stats manual](https://sa
 Plots will show:
 
 - Stats by non-reference allele frequency, depth distribution, stats by quality and per-sample counts, singleton stats, etc.
-- Note: When using [Strelka2](https://github.com/Illumina/strelka), there will be no depth distribution plot, as Strelka2 does not report the INFO/DP field
+- Note: When using [Strelka](https://github.com/Illumina/strelka), there will be no depth distribution plot, as Strelka does not report the INFO/DP field
 
 <details markdown="1">
 <summary>Output files for all samples</summary>

diff --git a/docs/usage.md b/docs/usage.md
@@ -452,7 +452,7 @@ For a thorough list, please refer the [Azure Sizes for virtual machines in Azure
 
 ## How to test the pipeline
 
-When using default parameters only, sarek runs preprocessing and `Strelka2`.
+When using default parameters only, sarek runs preprocessing and `Strelka`.
 This is reflected in the default test profile:
 
 ```bash
@@ -570,7 +570,7 @@ This list is by no means exhaustive and it will depend on the specific analysis
 | [GATK HaplotypeCaller](https://gatk.broadinstitute.org/hc/en-us/articles/5358864757787-HaplotypeCaller) |  x  |  x  |   x    |    x    |   -   |    -    |
 | [GATK Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/5358911630107-Mutect2)                 |  x  |  x  |   x    |    -    |   x   |    x    |
 | [mpileup](https://www.htslib.org/doc/samtools-mpileup.html)                                             |  x  |  x  |   x    |    x    |   x   |    -    |
-| [Strelka2](https://github.com/Illumina/strelka)                                                         |  x  |  x  |   x    |    x    |   x   |    x    |
+| [Strelka](https://github.com/Illumina/strelka)                                                          |  x  |  x  |   x    |    x    |   x   |    x    |
 | [Manta](https://github.com/Illumina/manta)                                                              |  x  |  x  |   x    |    x    |   x   |    x    |
 | [TIDDIT](https://github.com/SciLifeLab/TIDDIT)                                                          |  x  |  x  |   x    |    x    |   x   |    x    |
 | [ASCAT](https://github.com/VanLoo-lab/ascat)                                                            |  x  |  x  |   -    |    -    |   -   |    x    |

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -111,7 +111,7 @@
                     "type": "string",
                     "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: 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), 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`.",
+                    "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: 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, Strelka\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|freebayes|haplotypecaller|sentieon_dnascope|sentieon_haplotyper|manta|merge|mpileup|msisensorpro|mutect2|ngscheckmate|sentieon_dedup|snpeff|strelka|tiddit|vep)?,?)*(?<!,)$"
                 },
                 "skip_tools": {