From 6928c06e42da475fdd2f32b481e5d778f849ef38 Mon Sep 17 00:00:00 2001 From: Rike Date: Sat, 16 Jul 2022 23:10:30 +0200 Subject: [PATCH 1/3] remove sentieon leftovers --- nextflow.config | 5 ++--- nextflow_schema.json | 37 ++++++++++++++++++++++++------------- 2 files changed, 26 insertions(+), 16 deletions(-) diff --git a/nextflow.config b/nextflow.config index 271c849648..d997e3dc72 100644 --- a/nextflow.config +++ b/nextflow.config @@ -22,7 +22,6 @@ params { // Main options no_intervals = false // Intervals will be built from the fasta file nucleotides_per_second = 1000 // Default interval size - sentieon = false // Not using Sentieon by default tools = null // No default Variant_Calling or Annotation tools skip_tools = null // All tools (markduplicates + baserecalibrator + QC) are used by default @@ -64,8 +63,8 @@ params { cf_minqual = 0 // ControlFreec default values cf_window = null // by default we are not using this in Control-FREEC - pon = null // No default PON (Panel of Normals) file for GATK Mutect2 / Sentieon TNscope - pon_tbi = null // No default PON index for GATK Mutect2 / Sentieon TNscope + pon = null // No default PON (Panel of Normals) file for GATK Mutect2 + pon_tbi = null // No default PON index for GATK Mutect2 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 diff --git a/nextflow_schema.json b/nextflow_schema.json index 8d94a9b986..56cdc6edaf 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,7 +10,10 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": ["step", "outdir"], + "required": [ + "step", + "outdir" + ], "properties": { "step": { "type": "string", @@ -57,7 +60,7 @@ "type": "string", "fa_icon": "fas fa-toolbox", "description": "Tools to use for variant calling and/or for annotation.", - "help_text": "Multiple separated with commas.\n\nGermline variant calling can currently only be performed with the following variant callers:\n- FreeBayes, HaplotypeCaller, Manta, mpileup, Strelka, TIDDIT\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- ASCAT, Control-FREEC, FreeBayes, Manta, MSIsensorpro, Mutect2, Strelka\n\n**NB** Mutect2 for somatic variant calling cannot be combined with `--no_intervals`\n\nTumor-only somatic variant calling can currently only be performed with the following variant callers:\n- Control-FREEC, Manta, mpileup, Mutect2, TIDDIT\n\nAnnotation is done using snpEff, VEP, or even both consecutively.\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted.\n\n\n\n`DNAseq`, `DNAscope` and `TNscope` are only available with `--sentieon`\n\n> **NB** tools can be specified with no concern for case.", + "help_text": "Multiple separated with commas.\n\nGermline variant calling can currently only be performed with the following variant callers:\n- FreeBayes, HaplotypeCaller, Manta, mpileup, Strelka, TIDDIT\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- ASCAT, Control-FREEC, FreeBayes, Manta, MSIsensorpro, Mutect2, Strelka\n\n**NB** Mutect2 for somatic variant calling cannot be combined with `--no_intervals`\n\nTumor-only somatic variant calling can currently only be performed with the following variant callers:\n- Control-FREEC, Manta, mpileup, Mutect2, TIDDIT\n\nAnnotation is done using snpEff, VEP, or even both consecutively.\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted.\n\n> **NB** tools can be specified with no concern for case.", "pattern": "^((ascat|cnvkit|controlfreec|deepvariant|dnascope|dnaseq|freebayes|haplotypecaller|manta|merge|mpileup|msisensorpro|mutect2|snpeff|strelka|tiddit|tnscope|vep)*,?)*$" }, "no_intervals": { @@ -73,12 +76,6 @@ "help_text": "Intervals are part of the genome chopped up, used to speed up preprocessing and variant calling.", "default": 1000 }, - "sentieon": { - "type": "boolean", - "fa_icon": "fas fa-tools", - "description": "Enable Sentieon if available.", - "help_text": "Sentieon is a commercial solution to process genomics data with high computing efficiency, fast turnaround time, exceptional accuracy, and 100% consistency.\n\n> **NB** Adds the following tools for the `--tools` options: `DNAseq`, `DNAscope` and `TNscope`." - }, "skip_tools": { "type": "string", "fa_icon": "fas fa-forward", @@ -193,7 +190,11 @@ "type": "string", "default": "bwa-mem", "fa_icon": "fas fa-puzzle-piece", - "enum": ["bwa-mem", "bwa-mem2", "dragmap"], + "enum": [ + "bwa-mem", + "bwa-mem2", + "dragmap" + ], "description": "Specify aligner to be used to map reads to reference genome.", "help_text": "> **WARNING** Current indices for `bwa` in AWS iGenomes are not compatible with `bwa-mem2` and `dragmap`.\n> `Sarek` will build them automatically if not provided.\n\n> **WARNING** BWA-mem2 is in active development\n> Sarek might not be able to require the right amount of resources for it at the moment\n> We recommend to use pre-built indexes.", "hidden": true @@ -291,7 +292,7 @@ "pon": { "type": "string", "fa_icon": "fas fa-file", - "description": "Panel-of-normals VCF (bgzipped) for GATK Mutect2 / Sentieon TNscope.", + "description": "Panel-of-normals VCF (bgzipped) for GATK Mutect2", "help_text": "Without PON, there will be no calls with PASS in the INFO field, only an unfiltered VCF is written.\nIt is recommended to make your own PON, as it depends on sequencer and library preparation.\nFor tests in iGenomes there is a dummy PON file in the Annotation/GermlineResource directory, but it should not be used as a real PON file.\n\nSee [PON documentation](https://gatk.broadinstitute.org/hc/en-us/articles/360042479112-CreateSomaticPanelOfNormals-BETA)\n> **NB** PON file should be bgzipped." }, "pon_tbi": { @@ -319,7 +320,6 @@ "type": "boolean", "fa_icon": "fas fa-database", "description": "Allow usage of fasta file for annotation with VEP.\ncf https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#fasta", - "default": false, "hidden": true }, "vep_dbnsfp": { @@ -428,7 +428,11 @@ "type": "string", "default": "vcf", "description": "VEP output-file format.", - "enum": ["json", "tab", "vcf"], + "enum": [ + "json", + "tab", + "vcf" + ], "help_text": "Sets the format of the output-file from VEP. Available formats: json, tab and vcf.", "fa_icon": "fas fa-table" } @@ -769,7 +773,14 @@ "description": "Method used to save pipeline results to output directory.", "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", "fa_icon": "fas fa-copy", - "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "enum": [ + "symlink", + "rellink", + "link", + "copy", + "copyNoFollow", + "move" + ], "hidden": true }, "email": { From f8914fa60f37b990f1553bab7b40379a099d89de Mon Sep 17 00:00:00 2001 From: Rike Date: Sat, 16 Jul 2022 23:11:54 +0200 Subject: [PATCH 2/3] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 19d221a92c..ed0dc39ca3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -148,6 +148,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#562](https://github.com/nf-core/sarek/pull/562) - Restart from `--step annotate` from folder is removed. Use a `csv` file instead - [#571](https://github.com/nf-core/sarek/pull/571) - Removed the local module `concat_vcf`. - [#605](https://github.com/nf-core/sarek/pull/605) - Removed Scatter/gather from GATK_SINGLE_SAMPLE_GERMLINE_VARIANT_CALLING, all intervals are processed together +- [#643](https://github.com/nf-core/sarek/pull/643) - Removed Sentieon parameters ## [2.7.1](https://github.com/nf-core/sarek/releases/tag/2.7.1) - Pårtejekna From 674c8206e38dfc48eb63c31770b278cde025017c Mon Sep 17 00:00:00 2001 From: Rike Date: Sun, 17 Jul 2022 10:11:27 +0200 Subject: [PATCH 3/3] prettier --- nextflow_schema.json | 26 ++++---------------------- 1 file changed, 4 insertions(+), 22 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 56cdc6edaf..0a23d33f62 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,10 +10,7 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": [ - "step", - "outdir" - ], + "required": ["step", "outdir"], "properties": { "step": { "type": "string", @@ -190,11 +187,7 @@ "type": "string", "default": "bwa-mem", "fa_icon": "fas fa-puzzle-piece", - "enum": [ - "bwa-mem", - "bwa-mem2", - "dragmap" - ], + "enum": ["bwa-mem", "bwa-mem2", "dragmap"], "description": "Specify aligner to be used to map reads to reference genome.", "help_text": "> **WARNING** Current indices for `bwa` in AWS iGenomes are not compatible with `bwa-mem2` and `dragmap`.\n> `Sarek` will build them automatically if not provided.\n\n> **WARNING** BWA-mem2 is in active development\n> Sarek might not be able to require the right amount of resources for it at the moment\n> We recommend to use pre-built indexes.", "hidden": true @@ -428,11 +421,7 @@ "type": "string", "default": "vcf", "description": "VEP output-file format.", - "enum": [ - "json", - "tab", - "vcf" - ], + "enum": ["json", "tab", "vcf"], "help_text": "Sets the format of the output-file from VEP. Available formats: json, tab and vcf.", "fa_icon": "fas fa-table" } @@ -773,14 +762,7 @@ "description": "Method used to save pipeline results to output directory.", "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", "fa_icon": "fas fa-copy", - "enum": [ - "symlink", - "rellink", - "link", - "copy", - "copyNoFollow", - "move" - ], + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], "hidden": true }, "email": {