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

remove sentieon leftovers #643

Merged
merged 3 commits into from
Jul 17, 2022
Merged

remove sentieon leftovers #643

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
6928c06
remove sentieon leftovers
FriederikeHanssen Jul 16, 2022
f8914fa
update changelog
FriederikeHanssen Jul 16, 2022
674c820
prettier
FriederikeHanssen Jul 17, 2022
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 @@ -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

Expand Down
5 changes: 2 additions & 3 deletions nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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
Expand Down
11 changes: 2 additions & 9 deletions nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@
"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": {
Expand All @@ -73,12 +73,6 @@
"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",
Expand Down Expand Up @@ -291,7 +285,7 @@
"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": {
Expand Down Expand Up @@ -319,7 +313,6 @@
"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": {
Expand Down