Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix typo (strelka2 -> strelka) #1536

Merged
merged 6 commits into from
May 27, 2024
Merged

Fix typo (strelka2 -> strelka) #1536

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
4388c4d
fix(schema): fix typo (strelka2 -> strelka)
maxulysse May 22, 2024
623731c
fix(typo): strelka2 -> strelka
maxulysse May 27, 2024
7f0fabe
Merge branch 'dev' into dev
maxulysse May 27, 2024
f2cae49
merge
maxulysse May 27, 2024
444a229
merge
maxulysse May 27, 2024
7d6a0d6
fix merge conflicts
maxulysse May 27, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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`

Expand Down
12 changes: 6 additions & 6 deletions docs/output.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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">
Expand Down Expand Up @@ -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>
Expand Down Expand Up @@ -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>
Expand Down Expand Up @@ -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>
Expand Down
4 changes: 2 additions & 2 deletions docs/usage.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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 |
Expand Down
2 changes: 1 addition & 1 deletion nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand Down
Loading