From 4388c4dca4ce89af1aa491f83af2292ed984a45b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 22 May 2024 11:02:15 -0400 Subject: [PATCH 1/5] fix(schema): fix typo (strelka2 -> strelka) --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index c7deed767..0cac3eb49 100644 --- 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)?,?)*(? Date: Mon, 27 May 2024 13:30:18 +0200 Subject: [PATCH 2/5] fix(typo): strelka2 -> strelka --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 427054236..706d6388f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,8 @@ 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` + ### Removed ### Dependencies From f2cae492314ee2cf4b491bd08aa423b61af8b423 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 27 May 2024 13:33:35 +0200 Subject: [PATCH 3/5] merge --- CHANGELOG.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 938f432e6..812bca8b5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,11 +23,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed <<<<<<< dev -- [#1536](https://github.com/nf-core/sarek/pull/1536) - Correct typo `Strelka2` to `Strelka` -======= + +- # [#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` ->>>>>>> dev + > > > > > > > dev ### Removed From 444a229a4e9d1d843419245f21647fbbbdff4e79 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 27 May 2024 13:34:06 +0200 Subject: [PATCH 4/5] merge --- docs/output.md | 12 ++++++------ docs/usage.md | 4 ++-- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/output.md b/docs/output.md index ff6445e89..0f49c73ed 100644 --- 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 -#### 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).
@@ -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).
Output files for normal samples @@ -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.
Concatenated VCF-files for normal samples @@ -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
Output files for all samples diff --git a/docs/usage.md b/docs/usage.md index e54db35d3..f39e327bb 100644 --- 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 | From 7d6a0d63b28b1373bbaf395514d9ba8a77ec13a4 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 27 May 2024 13:34:58 +0200 Subject: [PATCH 5/5] fix merge conflicts --- CHANGELOG.md | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 812bca8b5..dc77e7639 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,12 +22,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed -<<<<<<< dev - -- # [#1536](https://github.com/nf-core/sarek/pull/1536) - Correct typo `Strelka2` to `Strelka` +- [#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` - > > > > > > > dev ### Removed