From afe882a9915c3109b325baedba7c2057fac69797 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Mon, 22 May 2023 12:04:42 +0100 Subject: [PATCH 1/7] Update pipeline overview --- CHANGELOG.md | 1 + README.md | 27 +++++++++++---- nextflow.config | 92 ++++++++++++++----------------------------------- 3 files changed, 46 insertions(+), 74 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f23cf0aeb4..4db1c88ebb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed +- [tbc] - Update pipeline summary - [#859](https://github.com/nf-core/sarek/pull/859) - Back to dev - [#860](https://github.com/nf-core/sarek/pull/860) - Replace local subworkflow with nf-core version - `vcf_annotate_snpeff` - [#865](https://github.com/nf-core/sarek/pull/865) - Replace local subworkflow with nf-core version - `vcf_annotate_ensemblvep` diff --git a/README.md b/README.md index dd49f72153..fdc00f09cb 100644 --- a/README.md +++ b/README.md @@ -33,13 +33,26 @@ It's listed on [Elixir - Tools and Data Services Registry](https://bio.tools/nf- By default, the pipeline currently performs the following: -- Sequencing quality control (`FastQC`) -- Map Reads to Reference (`BWA mem`) -- Mark Duplicates (`GATK MarkDuplicates`) -- Base (Quality Score) Recalibration (`GATK BaseRecalibrator`, `GATK ApplyBQSR`) -- Preprocessing quality control (`samtools stats`) -- Preprocessing quality control (`mosdepth`) -- Overall pipeline run summaries (`MultiQC`) +- Form consensus reads from UMI sequences (`fgbio`) +- Sequencing quality control and trimming (`FastQC`, `fastp`) +- Map Reads to Reference (_either:_ `BWA-mem`, `BWA-mem2`, `dragmap`) +- Preprocess BAM file (`GATK MarkDuplicates`, `GATK BaseRecalibrator`, `GATK ApplyBQSR`) +- Summarise alignment statistics (`samtools stats`, `mosdepth`) +- Variant calling (enabled by `--tools`, see [compatibility](https://github.com/nf-core/sarek/blob/master/docs/usage.md#which-variant-calling-tool-is-implemented-for-which-data-type)): + - `haplotypecaller` + - `freebayes` + - `mpileup` + - `strelka2` + - `deepvariant` + - `mutect2` + - `manta` + - `tiddit` + - `ASCAT` + - `Control-FREEC` + - `CNVkit` + - `MSIsensor-pro` +- Variant filtering and annotation (`GATK CNNScoreVariants`, `SnpEff`, `Ensembl VEP`) +- Summarise and represent QC (`MultiQC`)

diff --git a/nextflow.config b/nextflow.config index eecfb0cc8c..1631195706 100644 --- a/nextflow.config +++ b/nextflow.config @@ -14,16 +14,14 @@ params { step = 'mapping' // Starts with mapping // References - genome = 'GATK.GRCh38' - igenomes_base = 's3://ngi-igenomes/igenomes' - igenomes_ignore = false - save_reference = false // Built references not saved - build_only_index = false // Only build the reference indexes - download_cache = false // Do not download annotation cache + genome = 'GATK.GRCh38' + igenomes_base = 's3://ngi-igenomes/igenomes' + igenomes_ignore = false + save_reference = false // Built references not saved // Main options no_intervals = false // Intervals will be built from the fasta file - nucleotides_per_second = 200000 // Default interval size + nucleotides_per_second = 1000 // Default interval size tools = null // No default Variant_Calling or Annotation tools skip_tools = null // All tools (markduplicates + baserecalibrator + QC) are used by default split_fastq = 50000000 // FASTQ files will not be split by default by FASTP @@ -65,7 +63,6 @@ params { cf_minqual = 0 // ControlFreec default values cf_window = null // by default we are not using this in Control-FREEC cnvkit_reference = null // by default the reference is build from the fasta file - concatenate_vcfs = false // by default we don't concatenate the germline-vcf-files ignore_soft_clipped_bases = false // no --dont-use-soft-clipped-bases for GATK Mutect2 wes = false // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers joint_germline = false // g.vcf & joint germline calling are not run by default if HaplotypeCaller is selected @@ -84,7 +81,6 @@ params { spliceai_indel = null // No spliceai_indel file spliceai_indel_tbi = null // No spliceai_indel file index vep_spliceregion = null // spliceregion plugin disabled within VEP - outdir_cache = null // No output directory for cache snpeff_cache = null // No directory for snpEff cache vep_cache = null // No directory for VEP cache vep_include_fasta = false // Don't use fasta file for annotation with VEP @@ -97,7 +93,7 @@ params { multiqc_methods_description = null // Boilerplate options - outdir = null + outdir = 'results' tracedir = "${params.outdir}/pipeline_info" publish_dir_mode = 'copy' email = null @@ -106,10 +102,11 @@ params { monochrome_logs = false hook_url = null help = false - version = false validate_params = true show_hidden_params = false schema_ignore_params = 'genomes,snpeff_version,vep_version,cf_ploidy' + enable_conda = false + // Config options custom_config_version = 'master' @@ -118,7 +115,7 @@ params { config_profile_contact = null config_profile_url = null config_profile_name = null - test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek3' + // Max resource options // Defaults only, expecting to be overwritten @@ -145,25 +142,18 @@ try { } profiles { - debug { - cleanup = false - dumpHashes = true - process.beforeScript = 'echo $HOSTNAME' - } + debug { process.beforeScript = 'echo $HOSTNAME' } conda { - apptainer.enabled = false + params.enable_conda = true charliecloud.enabled = false - conda.enabled = true docker.enabled = false podman.enabled = false shifter.enabled = false singularity.enabled = false } mamba { - apptainer.enabled = false - charliecloud.enabled = false - conda.enabled = true conda.useMamba = true + params.enable_conda = true charliecloud.enabled = false docker.enabled = false podman.enabled = false @@ -171,59 +161,37 @@ profiles { singularity.enabled = false } docker { - apptainer.enabled = false - charliecloud.enabled = false - conda.enabled = false docker.enabled = true docker.userEmulation = { params.use_gatk_spark ? false : true }.call() + charliecloud.enabled = false podman.enabled = false shifter.enabled = false singularity.enabled = false } - arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' - } singularity { - apptainer.enabled = false + singularity.autoMounts = true + singularity.enabled = true charliecloud.enabled = false - conda.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false - singularity.autoMounts = true - singularity.enabled = true } podman { - apptainer.enabled = false + podman.enabled = true charliecloud.enabled = false - conda.enabled = false docker.enabled = false - podman.enabled = true shifter.enabled = false singularity.enabled = false } shifter { - apptainer.enabled = false + shifter.enabled = true charliecloud.enabled = false - conda.enabled = false docker.enabled = false podman.enabled = false - shifter.enabled = true singularity.enabled = false } charliecloud { - apptainer.enabled = false charliecloud.enabled = true - conda.enabled = false - docker.enabled = false - podman.enabled = false - shifter.enabled = false - singularity.enabled = false - } - apptainer { - apptainer.enabled = true - charliecloud.enabled = false - conda.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false @@ -287,12 +255,6 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] -// Set default registry for Docker and Podman independent of -profile -// Will not be used unless Docker / Podman are enabled -// Set to your registry if you have a mirror of containers -docker.registry = 'quay.io' -podman.registry = 'quay.io' - def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true @@ -313,12 +275,12 @@ dag { manifest { name = 'nf-core/sarek' - author = """Maxime Garcia, Szilveszter Juhos, Friederike Hanssen""" + author = 'Maxime Garcia, Szilveszter Juhos, Friederike Hanssen' homePage = 'https://github.com/nf-core/sarek' - description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing""" + description = 'An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing' mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' - version = '3.2dev' + nextflowVersion = '!>=21.10.3' + version = '3.1.2' doi = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683' } @@ -328,18 +290,17 @@ includeConfig 'conf/modules/modules.config' // Load more modules specific config for DSL2 module specific options // prepare reference -includeConfig 'conf/modules/prepare_cache.config' -includeConfig 'conf/modules/prepare_genome.config' includeConfig 'conf/modules/prepare_intervals.config' +includeConfig 'conf/modules/prepare_genome.config' // preprocessing -includeConfig 'conf/modules/aligner.config' includeConfig 'conf/modules/alignment_to_fastq.config' +includeConfig 'conf/modules/umi.config' +includeConfig 'conf/modules/trimming.config' +includeConfig 'conf/modules/aligner.config' includeConfig 'conf/modules/markduplicates.config' includeConfig 'conf/modules/prepare_recalibration.config' includeConfig 'conf/modules/recalibrate.config' -includeConfig 'conf/modules/trimming.config' -includeConfig 'conf/modules/umi.config' // variant calling includeConfig 'conf/modules/ascat.config' @@ -348,7 +309,6 @@ includeConfig 'conf/modules/controlfreec.config' includeConfig 'conf/modules/deepvariant.config' includeConfig 'conf/modules/freebayes.config' includeConfig 'conf/modules/haplotypecaller.config' -includeConfig 'conf/modules/joint_germline.config' includeConfig 'conf/modules/manta.config' includeConfig 'conf/modules/mpileup.config' includeConfig 'conf/modules/msisensorpro.config' @@ -356,8 +316,6 @@ includeConfig 'conf/modules/mutect2.config' includeConfig 'conf/modules/strelka.config' includeConfig 'conf/modules/tiddit.config' -includeConfig 'conf/modules/post_variant_calling.config' - //annotate includeConfig 'conf/modules/annotate.config' From 5e1d8f489487d0741b386c655146ebfef8990463 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Mon, 22 May 2023 12:06:33 +0100 Subject: [PATCH 2/7] Revert nextflow.config --- nextflow.config | 92 +++++++++++++++++++++++++++++++++++-------------- 1 file changed, 67 insertions(+), 25 deletions(-) diff --git a/nextflow.config b/nextflow.config index 1631195706..eecfb0cc8c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -14,14 +14,16 @@ params { step = 'mapping' // Starts with mapping // References - genome = 'GATK.GRCh38' - igenomes_base = 's3://ngi-igenomes/igenomes' - igenomes_ignore = false - save_reference = false // Built references not saved + genome = 'GATK.GRCh38' + igenomes_base = 's3://ngi-igenomes/igenomes' + igenomes_ignore = false + save_reference = false // Built references not saved + build_only_index = false // Only build the reference indexes + download_cache = false // Do not download annotation cache // Main options no_intervals = false // Intervals will be built from the fasta file - nucleotides_per_second = 1000 // Default interval size + nucleotides_per_second = 200000 // Default interval size tools = null // No default Variant_Calling or Annotation tools skip_tools = null // All tools (markduplicates + baserecalibrator + QC) are used by default split_fastq = 50000000 // FASTQ files will not be split by default by FASTP @@ -63,6 +65,7 @@ params { cf_minqual = 0 // ControlFreec default values cf_window = null // by default we are not using this in Control-FREEC cnvkit_reference = null // by default the reference is build from the fasta file + concatenate_vcfs = false // by default we don't concatenate the germline-vcf-files ignore_soft_clipped_bases = false // no --dont-use-soft-clipped-bases for GATK Mutect2 wes = false // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers joint_germline = false // g.vcf & joint germline calling are not run by default if HaplotypeCaller is selected @@ -81,6 +84,7 @@ params { spliceai_indel = null // No spliceai_indel file spliceai_indel_tbi = null // No spliceai_indel file index vep_spliceregion = null // spliceregion plugin disabled within VEP + outdir_cache = null // No output directory for cache snpeff_cache = null // No directory for snpEff cache vep_cache = null // No directory for VEP cache vep_include_fasta = false // Don't use fasta file for annotation with VEP @@ -93,7 +97,7 @@ params { multiqc_methods_description = null // Boilerplate options - outdir = 'results' + outdir = null tracedir = "${params.outdir}/pipeline_info" publish_dir_mode = 'copy' email = null @@ -102,11 +106,10 @@ params { monochrome_logs = false hook_url = null help = false + version = false validate_params = true show_hidden_params = false schema_ignore_params = 'genomes,snpeff_version,vep_version,cf_ploidy' - enable_conda = false - // Config options custom_config_version = 'master' @@ -115,7 +118,7 @@ params { config_profile_contact = null config_profile_url = null config_profile_name = null - + test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek3' // Max resource options // Defaults only, expecting to be overwritten @@ -142,18 +145,25 @@ try { } profiles { - debug { process.beforeScript = 'echo $HOSTNAME' } + debug { + cleanup = false + dumpHashes = true + process.beforeScript = 'echo $HOSTNAME' + } conda { - params.enable_conda = true + apptainer.enabled = false charliecloud.enabled = false + conda.enabled = true docker.enabled = false podman.enabled = false shifter.enabled = false singularity.enabled = false } mamba { + apptainer.enabled = false + charliecloud.enabled = false + conda.enabled = true conda.useMamba = true - params.enable_conda = true charliecloud.enabled = false docker.enabled = false podman.enabled = false @@ -161,37 +171,59 @@ profiles { singularity.enabled = false } docker { + apptainer.enabled = false + charliecloud.enabled = false + conda.enabled = false docker.enabled = true docker.userEmulation = { params.use_gatk_spark ? false : true }.call() - charliecloud.enabled = false podman.enabled = false shifter.enabled = false singularity.enabled = false } + arm { + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + } singularity { - singularity.autoMounts = true - singularity.enabled = true + apptainer.enabled = false charliecloud.enabled = false + conda.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false + singularity.autoMounts = true + singularity.enabled = true } podman { - podman.enabled = true + apptainer.enabled = false charliecloud.enabled = false + conda.enabled = false docker.enabled = false + podman.enabled = true shifter.enabled = false singularity.enabled = false } shifter { - shifter.enabled = true + apptainer.enabled = false charliecloud.enabled = false + conda.enabled = false docker.enabled = false podman.enabled = false + shifter.enabled = true singularity.enabled = false } charliecloud { + apptainer.enabled = false charliecloud.enabled = true + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + singularity.enabled = false + } + apptainer { + apptainer.enabled = true + charliecloud.enabled = false + conda.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false @@ -255,6 +287,12 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set default registry for Docker and Podman independent of -profile +// Will not be used unless Docker / Podman are enabled +// Set to your registry if you have a mirror of containers +docker.registry = 'quay.io' +podman.registry = 'quay.io' + def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true @@ -275,12 +313,12 @@ dag { manifest { name = 'nf-core/sarek' - author = 'Maxime Garcia, Szilveszter Juhos, Friederike Hanssen' + author = """Maxime Garcia, Szilveszter Juhos, Friederike Hanssen""" homePage = 'https://github.com/nf-core/sarek' - description = 'An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing' + description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing""" mainScript = 'main.nf' - nextflowVersion = '!>=21.10.3' - version = '3.1.2' + nextflowVersion = '!>=22.10.1' + version = '3.2dev' doi = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683' } @@ -290,17 +328,18 @@ includeConfig 'conf/modules/modules.config' // Load more modules specific config for DSL2 module specific options // prepare reference -includeConfig 'conf/modules/prepare_intervals.config' +includeConfig 'conf/modules/prepare_cache.config' includeConfig 'conf/modules/prepare_genome.config' +includeConfig 'conf/modules/prepare_intervals.config' // preprocessing -includeConfig 'conf/modules/alignment_to_fastq.config' -includeConfig 'conf/modules/umi.config' -includeConfig 'conf/modules/trimming.config' includeConfig 'conf/modules/aligner.config' +includeConfig 'conf/modules/alignment_to_fastq.config' includeConfig 'conf/modules/markduplicates.config' includeConfig 'conf/modules/prepare_recalibration.config' includeConfig 'conf/modules/recalibrate.config' +includeConfig 'conf/modules/trimming.config' +includeConfig 'conf/modules/umi.config' // variant calling includeConfig 'conf/modules/ascat.config' @@ -309,6 +348,7 @@ includeConfig 'conf/modules/controlfreec.config' includeConfig 'conf/modules/deepvariant.config' includeConfig 'conf/modules/freebayes.config' includeConfig 'conf/modules/haplotypecaller.config' +includeConfig 'conf/modules/joint_germline.config' includeConfig 'conf/modules/manta.config' includeConfig 'conf/modules/mpileup.config' includeConfig 'conf/modules/msisensorpro.config' @@ -316,6 +356,8 @@ includeConfig 'conf/modules/mutect2.config' includeConfig 'conf/modules/strelka.config' includeConfig 'conf/modules/tiddit.config' +includeConfig 'conf/modules/post_variant_calling.config' + //annotate includeConfig 'conf/modules/annotate.config' From 088dead20ff761670473e749835253d647dddd9b Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Mon, 22 May 2023 12:08:58 +0100 Subject: [PATCH 3/7] Slight change to format --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index fdc00f09cb..c58b62a3da 100644 --- a/README.md +++ b/README.md @@ -35,8 +35,8 @@ By default, the pipeline currently performs the following: - Form consensus reads from UMI sequences (`fgbio`) - Sequencing quality control and trimming (`FastQC`, `fastp`) -- Map Reads to Reference (_either:_ `BWA-mem`, `BWA-mem2`, `dragmap`) -- Preprocess BAM file (`GATK MarkDuplicates`, `GATK BaseRecalibrator`, `GATK ApplyBQSR`) +- Map Reads to Reference (`BWA-mem` or `BWA-mem2` or `dragmap`) +- Process BAM file (`GATK MarkDuplicates`, `GATK BaseRecalibrator`, `GATK ApplyBQSR`) - Summarise alignment statistics (`samtools stats`, `mosdepth`) - Variant calling (enabled by `--tools`, see [compatibility](https://github.com/nf-core/sarek/blob/master/docs/usage.md#which-variant-calling-tool-is-implemented-for-which-data-type)): - `haplotypecaller` From ee4168c4c7cb2f596a8ee6ce34162c4150c5269b Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Mon, 22 May 2023 12:09:07 +0100 Subject: [PATCH 4/7] CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4db1c88ebb..85e2073012 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,7 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed -- [tbc] - Update pipeline summary +- [#1031](https://github.com/nf-core/sarek/pull/1031) - Update pipeline summary - [#859](https://github.com/nf-core/sarek/pull/859) - Back to dev - [#860](https://github.com/nf-core/sarek/pull/860) - Replace local subworkflow with nf-core version - `vcf_annotate_snpeff` - [#865](https://github.com/nf-core/sarek/pull/865) - Replace local subworkflow with nf-core version - `vcf_annotate_ensemblvep` From cfd9a745283c306ea92e081cb8f3d672e18f23ea Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Mon, 22 May 2023 12:14:03 +0100 Subject: [PATCH 5/7] CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 85e2073012..80b253e53e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,7 +21,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed -- [#1031](https://github.com/nf-core/sarek/pull/1031) - Update pipeline summary - [#859](https://github.com/nf-core/sarek/pull/859) - Back to dev - [#860](https://github.com/nf-core/sarek/pull/860) - Replace local subworkflow with nf-core version - `vcf_annotate_snpeff` - [#865](https://github.com/nf-core/sarek/pull/865) - Replace local subworkflow with nf-core version - `vcf_annotate_ensemblvep` @@ -40,6 +39,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1014](https://github.com/nf-core/sarek/pull/1014) - `snpeff_db` is now only the `db` version and not `genome.db` - [#1015](https://github.com/nf-core/sarek/pull/1015) - Increase default value for `--nucleotides_per_second` to `200000` resulting in 21 groups for `GATK.GRCh38` - [#1019](https://github.com/nf-core/sarek/pull/1019) - Set a default registry outside of profile scope +- [#1031](https://github.com/nf-core/sarek/pull/1031) - Update pipeline summary ### Fixed From e428d439b116c2417da9c9dd589d7b1be433b419 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Mon, 22 May 2023 16:48:12 +0100 Subject: [PATCH 6/7] Change wording of the pipeline summary...summary --- README.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index c58b62a3da..05b31cb079 100644 --- a/README.md +++ b/README.md @@ -31,7 +31,7 @@ It's listed on [Elixir - Tools and Data Services Registry](https://bio.tools/nf- ## Pipeline summary -By default, the pipeline currently performs the following: +Depending on the options and samples provided, the pipeline can currently perform the following: - Form consensus reads from UMI sequences (`fgbio`) - Sequencing quality control and trimming (`FastQC`, `fastp`) @@ -39,19 +39,19 @@ By default, the pipeline currently performs the following: - Process BAM file (`GATK MarkDuplicates`, `GATK BaseRecalibrator`, `GATK ApplyBQSR`) - Summarise alignment statistics (`samtools stats`, `mosdepth`) - Variant calling (enabled by `--tools`, see [compatibility](https://github.com/nf-core/sarek/blob/master/docs/usage.md#which-variant-calling-tool-is-implemented-for-which-data-type)): - - `haplotypecaller` + - `HaplotypeCaller` - `freebayes` - `mpileup` - - `strelka2` - - `deepvariant` - - `mutect2` - - `manta` - - `tiddit` + - `Strelka2` + - `DeepVariant` + - `Mutect2` + - `Manta` + - `TIDDIT` - `ASCAT` - `Control-FREEC` - `CNVkit` - `MSIsensor-pro` -- Variant filtering and annotation (`GATK CNNScoreVariants`, `SnpEff`, `Ensembl VEP`) +- Variant filtering and annotation (`GATK CNNScoreVariants`, `GATK FilterMutectCalls`, `SnpEff`, `Ensembl VEP`) - Summarise and represent QC (`MultiQC`)

From 7779dc592fcd55d1dbd274caa3713f98791ab930 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Mon, 22 May 2023 16:53:11 +0100 Subject: [PATCH 7/7] Remove VCF filtering tools --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 05b31cb079..55e8367aff 100644 --- a/README.md +++ b/README.md @@ -51,7 +51,7 @@ Depending on the options and samples provided, the pipeline can currently perfor - `Control-FREEC` - `CNVkit` - `MSIsensor-pro` -- Variant filtering and annotation (`GATK CNNScoreVariants`, `GATK FilterMutectCalls`, `SnpEff`, `Ensembl VEP`) +- Variant filtering and annotation (`SnpEff`, `Ensembl VEP`) - Summarise and represent QC (`MultiQC`)