From c7bb43b8ed08f1f9c7cb2f025eccb941aad4d2f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Wed, 28 Aug 2024 14:55:38 +0200 Subject: [PATCH 1/9] update table for implemented modes --- docs/usage.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 6a91830492..bfb941fe2f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -575,20 +575,20 @@ Sarek can be started at different points in the analysis by setting the paramete This list is by no means exhaustive and it will depend on the specific analysis you would like to run. This is a suggestion based on the individual docs of the tools specifically for human genomes and a garden-variety sequencing run as well as what has been added to the pipeline. -| Tool | WGS | WES |  Panel |  Normal | Tumor | Somatic | +| Tool | WGS | WES |  Panel |  Germline | Tumor-Only | Somatic (Tumor-Normal) | | :------------------------------------------------------------------------------------------------------ | :-: | :-: | :----: | :-----: | :---: | :-----: | | [DeepVariant](https://github.com/google/deepvariant) | x | x | x | x | - | - | | [FreeBayes](https://github.com/ekg/freebayes) | x | x | x | x | x | x | | [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 | - | -| [Strelka](https://github.com/Illumina/strelka) | x | x | x | x | x | x | +| [Strelka](https://github.com/Illumina/strelka) | 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 | | [CNVKit](https://cnvkit.readthedocs.io/en/stable/) | x | x | - | x | x | x | | [Control-FREEC](https://github.com/BoevaLab/FREEC) | x | x | x | - | x | x | -| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | - | x | +| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | x | x | ## How to run ASCAT with whole-exome sequencing data? From 41bd3ca407161a4250c473462e57b75d884ab8c5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Wed, 28 Aug 2024 14:57:36 +0200 Subject: [PATCH 2/9] format table --- docs/usage.md | 29 +++++++++++++++-------------- 1 file changed, 15 insertions(+), 14 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index bfb941fe2f..73c4690b6c 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -575,20 +575,21 @@ Sarek can be started at different points in the analysis by setting the paramete This list is by no means exhaustive and it will depend on the specific analysis you would like to run. This is a suggestion based on the individual docs of the tools specifically for human genomes and a garden-variety sequencing run as well as what has been added to the pipeline. -| Tool | WGS | WES |  Panel |  Germline | Tumor-Only | Somatic (Tumor-Normal) | -| :------------------------------------------------------------------------------------------------------ | :-: | :-: | :----: | :-----: | :---: | :-----: | -| [DeepVariant](https://github.com/google/deepvariant) | x | x | x | x | - | - | -| [FreeBayes](https://github.com/ekg/freebayes) | x | x | x | x | x | x | -| [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 | - | -| [Strelka](https://github.com/Illumina/strelka) | 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 | -| [CNVKit](https://cnvkit.readthedocs.io/en/stable/) | x | x | - | x | x | x | -| [Control-FREEC](https://github.com/BoevaLab/FREEC) | x | x | x | - | x | x | -| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | x | x | +| Tool | WGS | WES | Panel | Germline | Tumor-Only | Somatic (Tumor-Normal) | +|-:-------------------------------------------------------------------------------------------------------|-:-:-|-:-:-|-:-:---|-:-:------|-:-:--------|-:-:--------------------| +| [DeepVariant](https://github.com/google/deepvariant) | x | x | x | x | - | - | +| [FreeBayes](https://github.com/ekg/freebayes) | x | x | x | x | x | x | +| [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 | - | +| [Strelka](https://github.com/Illumina/strelka) | 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 | +| [CNVKit](https://cnvkit.readthedocs.io/en/stable/) | x | x | - | x | x | x | +| [Control-FREEC](https://github.com/BoevaLab/FREEC) | x | x | x | - | x | x | +| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | x | x | + ## How to run ASCAT with whole-exome sequencing data? From 1a9aa6e1a426793550186c4864d911b224b1b257 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Wed, 28 Aug 2024 15:01:08 +0200 Subject: [PATCH 3/9] format table --- docs/usage.md | 29 ++++++++++++++--------------- 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 73c4690b6c..bfb941fe2f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -575,21 +575,20 @@ Sarek can be started at different points in the analysis by setting the paramete This list is by no means exhaustive and it will depend on the specific analysis you would like to run. This is a suggestion based on the individual docs of the tools specifically for human genomes and a garden-variety sequencing run as well as what has been added to the pipeline. -| Tool | WGS | WES | Panel | Germline | Tumor-Only | Somatic (Tumor-Normal) | -|-:-------------------------------------------------------------------------------------------------------|-:-:-|-:-:-|-:-:---|-:-:------|-:-:--------|-:-:--------------------| -| [DeepVariant](https://github.com/google/deepvariant) | x | x | x | x | - | - | -| [FreeBayes](https://github.com/ekg/freebayes) | x | x | x | x | x | x | -| [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 | - | -| [Strelka](https://github.com/Illumina/strelka) | 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 | -| [CNVKit](https://cnvkit.readthedocs.io/en/stable/) | x | x | - | x | x | x | -| [Control-FREEC](https://github.com/BoevaLab/FREEC) | x | x | x | - | x | x | -| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | x | x | - +| Tool | WGS | WES |  Panel |  Germline | Tumor-Only | Somatic (Tumor-Normal) | +| :------------------------------------------------------------------------------------------------------ | :-: | :-: | :----: | :-----: | :---: | :-----: | +| [DeepVariant](https://github.com/google/deepvariant) | x | x | x | x | - | - | +| [FreeBayes](https://github.com/ekg/freebayes) | x | x | x | x | x | x | +| [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 | - | +| [Strelka](https://github.com/Illumina/strelka) | 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 | +| [CNVKit](https://cnvkit.readthedocs.io/en/stable/) | x | x | - | x | x | x | +| [Control-FREEC](https://github.com/BoevaLab/FREEC) | x | x | x | - | x | x | +| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | x | x | ## How to run ASCAT with whole-exome sequencing data? From c56ba54bc5fd8e231c67d92c95cef0902a0c5734 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Wed, 28 Aug 2024 15:04:03 +0200 Subject: [PATCH 4/9] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c9714a2519..60064c1129 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [1623](https://github.com/nf-core/sarek/pull/1623) - Update docs to clarify vep cache folder organisation - [1628](https://github.com/nf-core/sarek/pull/1628) - Fix dbsnp channel mapping in germline variant calling subworkflow +- [1635](https://github.com/nf-core/sarek/pull/1635) - Fix docs to reflect variant calling tool - data type correctly ### Removed From fe06ed9a68ca9bc2a592350921e4f4f943e37107 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Wed, 28 Aug 2024 15:05:14 +0200 Subject: [PATCH 5/9] prettier --- docs/usage.md | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index bfb941fe2f..255856d86f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -576,19 +576,19 @@ Sarek can be started at different points in the analysis by setting the paramete This list is by no means exhaustive and it will depend on the specific analysis you would like to run. This is a suggestion based on the individual docs of the tools specifically for human genomes and a garden-variety sequencing run as well as what has been added to the pipeline. | Tool | WGS | WES |  Panel |  Germline | Tumor-Only | Somatic (Tumor-Normal) | -| :------------------------------------------------------------------------------------------------------ | :-: | :-: | :----: | :-----: | :---: | :-----: | -| [DeepVariant](https://github.com/google/deepvariant) | x | x | x | x | - | - | -| [FreeBayes](https://github.com/ekg/freebayes) | x | x | x | x | x | x | -| [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 | - | -| [Strelka](https://github.com/Illumina/strelka) | 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 | -| [CNVKit](https://cnvkit.readthedocs.io/en/stable/) | x | x | - | x | x | x | -| [Control-FREEC](https://github.com/BoevaLab/FREEC) | x | x | x | - | x | x | -| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | x | x | +| :------------------------------------------------------------------------------------------------------ | :-: | :-: | :----: | :-------: | :--------: | :--------------------: | +| [DeepVariant](https://github.com/google/deepvariant) | x | x | x | x | - | - | +| [FreeBayes](https://github.com/ekg/freebayes) | x | x | x | x | x | x | +| [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 | - | +| [Strelka](https://github.com/Illumina/strelka) | 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 | +| [CNVKit](https://cnvkit.readthedocs.io/en/stable/) | x | x | - | x | x | x | +| [Control-FREEC](https://github.com/BoevaLab/FREEC) | x | x | x | - | x | x | +| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | x | x | ## How to run ASCAT with whole-exome sequencing data? From 1ccf16b258c47e0d01955a0138ab16cd3082eca3 Mon Sep 17 00:00:00 2001 From: Friederike Hanssen Date: Tue, 10 Dec 2024 10:00:38 +0100 Subject: [PATCH 6/9] Update docs/usage.md Co-authored-by: Maxime U Garcia --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 255856d86f..16b55b3c2b 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -588,7 +588,7 @@ This list is by no means exhaustive and it will depend on the specific analysis | [ASCAT](https://github.com/VanLoo-lab/ascat) | x | x | - | - | - | x | | [CNVKit](https://cnvkit.readthedocs.io/en/stable/) | x | x | - | x | x | x | | [Control-FREEC](https://github.com/BoevaLab/FREEC) | x | x | x | - | x | x | -| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | x | x | +| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | - | x | ## How to run ASCAT with whole-exome sequencing data? From e40d91da9091b2c16d889767107f2e842a1c93ca Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 10 Dec 2024 09:43:19 +0000 Subject: [PATCH 7/9] [automated] Fix code linting --- docs/usage.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index f2d6ceccc1..6ad2451887 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -581,7 +581,7 @@ This list is by no means exhaustive and it will depend on the specific analysis | [FreeBayes](https://github.com/ekg/freebayes) | x | x | x | x | x | x | | [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 | -| [lofreq](https://github.com/CSB5/lofreq) | x | x | x | - | x | - | +| [lofreq](https://github.com/CSB5/lofreq) | x | x | x | - | x | - | | [mpileup](https://www.htslib.org/doc/samtools-mpileup.html) | x | x | x | x | x | - | | [Strelka](https://github.com/Illumina/strelka) | x | x | x | x | - | x | | [Manta](https://github.com/Illumina/manta) | x | x | x | x | x | x | @@ -591,7 +591,6 @@ This list is by no means exhaustive and it will depend on the specific analysis | [Control-FREEC](https://github.com/BoevaLab/FREEC) | x | x | x | - | x | x | | [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro) | x | x | x | - | - | x | - ## How to run ASCAT with whole-exome sequencing data? ASCAT runs out of the box on whole genome sequencing data using iGenomes resources. While the ASCAT implementation in sarek is capable of running with whole-exome sequencing data, the needed references are currently not provided with the igenomes.config. According to the [developers](https://github.com/VanLoo-lab/ascat/issues/97) of ASCAT, loci and allele files (one file per chromosome) can be downloaded directly from the [Battenberg repository](https://ora.ox.ac.uk/objects/uuid:08e24957-7e76-438a-bd38-66c48008cf52). From ed95c839c0c193d0df8639feb918d847e42b9f54 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Tue, 10 Dec 2024 09:55:43 +0000 Subject: [PATCH 8/9] move entry to correct section --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 47d501d867..8e2d4f4e6a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed - [1579](https://github.com/nf-core/sarek/pull/1579) - Update Sentieon usage docs +- [1635](https://github.com/nf-core/sarek/pull/1635) - Fix docs to reflect variant calling tool - data type correctly - [1668](https://github.com/nf-core/sarek/pull/1668) - Add nf-test sharding CI - [1669](https://github.com/nf-core/sarek/pull/1669) - Better nf-test pipeline level tests - [1677](https://github.com/nf-core/sarek/pull/1677) - Migrate pytest aligner and pipeline default tests to nf-test From ae24b7f10e0bbdf9dc1b2c38aa006da3c43eb200 Mon Sep 17 00:00:00 2001 From: Friederike Hanssen Date: Tue, 10 Dec 2024 11:12:06 +0100 Subject: [PATCH 9/9] Update CHANGELOG.md --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8e2d4f4e6a..aa3eeb44f7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -99,7 +99,6 @@ Ruopsokjåkhå is another peak of the Pårte massif. - [1623](https://github.com/nf-core/sarek/pull/1623) - Update docs to clarify vep cache folder organisation - [1628](https://github.com/nf-core/sarek/pull/1628) - Fix dbsnp channel mapping in germline variant calling subworkflow -- [1635](https://github.com/nf-core/sarek/pull/1635) - Fix docs to reflect variant calling tool - data type correctly ### Removed