From 6dd5f0a3befd94ee658ef1845011338065fe2f70 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 13 Aug 2024 16:38:56 +0200 Subject: [PATCH 1/3] Corrects usage docs --- docs/usage.md | 65 ++++++++++++++++++++++++++------------------------- 1 file changed, 33 insertions(+), 32 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 66d0b357..259531ba 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -10,24 +10,24 @@ Table of contents: - [Run nf-core/raredisease with test data](#run-nf-coreraredisease-with-test-data) - [Updating the pipeline](#updating-the-pipeline) - [Run nf-core/raredisease with your data](#run-nf-coreraredisease-with-your-data) - - [Samplesheet](#samplesheet) - - [Reference files and parameters](#reference-files-and-parameters) - - [1. Alignment](#1-alignment) - - [2. QC stats from the alignment files](#2-qc-stats-from-the-alignment-files) - - [3. Repeat expansions](#3-repeat-expansions) - - [4. Variant calling - SNV](#4-variant-calling---snv) - - [5. Variant calling - Structural variants](#5-variant-calling---structural-variants) - - [6. Copy number variant calling](#6-copy-number-variant-calling) - - [7. SNV annotation \& Ranking](#7-snv-annotation--ranking) - - [8. SV annotation \& Ranking](#8-sv-annotation--ranking) - - [9. Mitochondrial annotation](#9-mitochondrial-annotation) - - [10. Mobile element calling](#10-mobile-element-calling) - - [11. Mobile element annotation](#11-mobile-element-annotation) - - [12. Variant evaluation](#12-variant-evaluation) - - [13. Prepare data for CNV visualisation in Gens](#13-prepare-data-for-cnv-visualisation-in-gens) - - [Run the pipeline](#run-the-pipeline) - - [Direct input in CLI](#direct-input-in-cli) - - [Import from a config file (recommended)](#import-from-a-config-file-recommended) + - [Samplesheet](#samplesheet) + - [Reference files and parameters](#reference-files-and-parameters) + - [1. Alignment](#1-alignment) + - [2. QC stats from the alignment files](#2-qc-stats-from-the-alignment-files) + - [3. Repeat expansions](#3-repeat-expansions) + - [4. Variant calling - SNV](#4-variant-calling---snv) + - [5. Variant calling - Structural variants](#5-variant-calling---structural-variants) + - [6. Copy number variant calling](#6-copy-number-variant-calling) + - [7. SNV annotation \& Ranking](#7-snv-annotation--ranking) + - [8. SV annotation \& Ranking](#8-sv-annotation--ranking) + - [9. Mitochondrial annotation](#9-mitochondrial-annotation) + - [10. Mobile element calling](#10-mobile-element-calling) + - [11. Mobile element annotation](#11-mobile-element-annotation) + - [12. Variant evaluation](#12-variant-evaluation) + - [13. Prepare data for CNV visualisation in Gens](#13-prepare-data-for-cnv-visualisation-in-gens) + - [Run the pipeline](#run-the-pipeline) + - [Direct input in CLI](#direct-input-in-cli) + - [Import from a config file (recommended)](#import-from-a-config-file-recommended) - [Best practices](#best-practices) - [Core Nextflow arguments](#core-nextflow-arguments) - [`-profile`](#-profile) @@ -228,16 +228,17 @@ The mandatory and optional parameters for each category are tabulated below. ##### 7. SNV annotation & Ranking -| Mandatory | Optional | -| ------------------------------------ | --------------------------------------------- | -| genome1 | reduced_penetrance8 | -| vcfanno_resources2 | vcfanno_lua | -| vcfanno_toml3 | vep_filters/vep_filters_scout_fmt9 | -| vep_cache_version | cadd_resources10 | -| vep_cache4 | vep_plugin_files11 | -| gnomad_af5 | | -| score_config_snv6 | | -| variant_consequences_snv7 | | +| Mandatory | Optional | +| ------------------------------------ | ---------------------------------------------- | +| genome1 | reduced_penetrance9 | +| vcfanno_resources2 | vcfanno_lua | +| vcfanno_toml3 | vep_filters/vep_filters_scout_fmt10 | +| vep_cache_version | cadd_resources11 | +| vep_cache4 | | +| gnomad_af5 | | +| score_config_snv6 | | +| variant_consequences_snv7 | | +| vep_plugin_files8 | | 1Genome version is used by VEP. You have the option to choose between GRCh37 and GRCh38.
2Path to VCF files and their indices used by vcfanno. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/vcfanno_resources.txt).
@@ -249,10 +250,10 @@ See example cache [here](https://raw.githubusercontent.com/nf-core/test-datasets no header and the following columns: `CHROM POS REF_ALLELE ALT_ALLELE AF`. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/gnomad_reformated.tab.gz).
6Used by GENMOD for ranking the variants. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/rank_model_snv.ini).
7File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic and mitochondrial SNVs. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/variant_consequences_v2.txt). You can learn more about these terms [here](https://grch37.ensembl.org/info/genome/variation/prediction/predicted_data.html). -8Used by GENMOD while modeling the variants. Contains a list of loci that show [reduced penetrance](https://medlineplus.gov/genetics/understanding/inheritance/penetranceexpressivity/) in people. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/reduced_penetrance.tsv).
-9 This file contains a list of candidate genes (with [HGNC](https://www.genenames.org/) IDs) that is used to split the variants into canditate variants and research variants. Research variants contain all the variants, while candidate variants are a subset of research variants and are associated with candidate genes. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/hgnc.txt). Not required if --skip_vep_filter is set to true.
-10Path to a folder containing cadd annotations. Equivalent of the data/annotations/ folder described [here](https://github.com/kircherlab/CADD-scripts/#manual-installation), and it is used to calculate CADD scores for small indels.
-11A CSV file that describes the files used by VEP's named and custom plugins. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/vep_files.csv).
+8A CSV file that describes the files used by VEP's named and custom plugins. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/vep_files.csv).
+9Used by GENMOD while modeling the variants. Contains a list of loci that show [reduced penetrance](https://medlineplus.gov/genetics/understanding/inheritance/penetranceexpressivity/) in people. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/reduced_penetrance.tsv).
+10 This file contains a list of candidate genes (with [HGNC](https://www.genenames.org/) IDs) that is used to split the variants into canditate variants and research variants. Research variants contain all the variants, while candidate variants are a subset of research variants and are associated with candidate genes. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/hgnc.txt). Not required if --skip_vep_filter is set to true.
+11Path to a folder containing cadd annotations. Equivalent of the data/annotations/ folder described [here](https://github.com/kircherlab/CADD-scripts/#manual-installation), and it is used to calculate CADD scores for small indels.
:::note We use CADD only to annotate small indels. To annotate SNVs with precomputed CADD scores, pass the file containing CADD scores as a resource to vcfanno instead. Files containing the precomputed CADD scores for SNVs can be downloaded from [here](https://cadd.gs.washington.edu/download) (download files listed under the description: "All possible SNVs of GRCh3<7/8>/hg3<7/8>") From 0c5b700661186023c11db65f5e32658d11fc4b5b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 13 Aug 2024 16:41:30 +0200 Subject: [PATCH 2/3] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2c4667bd..5d009cda 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- Update docs to show 'vep_plugin_files' as a mandatory parameter for SNV annotation [#594](https://github.com/nf-core/raredisease/issues/593) - Error in SVDB merge when only a single SV caller is run [#586](https://github.com/nf-core/raredisease/pull/586) - Errors due to misplaced version statements [#578](https://github.com/nf-core/raredisease/pull/578) - Stub crashes due to peddy reported in [#566](https://github.com/nf-core/raredisease/issues/566) [#576](https://github.com/nf-core/raredisease/pull/576] From 151e909a8d9516faf325150fc26bdc25aeda3292 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 13 Aug 2024 16:44:23 +0200 Subject: [PATCH 3/3] fix lint --- docs/usage.md | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 259531ba..5a110ad1 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -10,24 +10,24 @@ Table of contents: - [Run nf-core/raredisease with test data](#run-nf-coreraredisease-with-test-data) - [Updating the pipeline](#updating-the-pipeline) - [Run nf-core/raredisease with your data](#run-nf-coreraredisease-with-your-data) - - [Samplesheet](#samplesheet) - - [Reference files and parameters](#reference-files-and-parameters) - - [1. Alignment](#1-alignment) - - [2. QC stats from the alignment files](#2-qc-stats-from-the-alignment-files) - - [3. Repeat expansions](#3-repeat-expansions) - - [4. Variant calling - SNV](#4-variant-calling---snv) - - [5. Variant calling - Structural variants](#5-variant-calling---structural-variants) - - [6. Copy number variant calling](#6-copy-number-variant-calling) - - [7. SNV annotation \& Ranking](#7-snv-annotation--ranking) - - [8. SV annotation \& Ranking](#8-sv-annotation--ranking) - - [9. Mitochondrial annotation](#9-mitochondrial-annotation) - - [10. Mobile element calling](#10-mobile-element-calling) - - [11. Mobile element annotation](#11-mobile-element-annotation) - - [12. Variant evaluation](#12-variant-evaluation) - - [13. Prepare data for CNV visualisation in Gens](#13-prepare-data-for-cnv-visualisation-in-gens) - - [Run the pipeline](#run-the-pipeline) - - [Direct input in CLI](#direct-input-in-cli) - - [Import from a config file (recommended)](#import-from-a-config-file-recommended) + - [Samplesheet](#samplesheet) + - [Reference files and parameters](#reference-files-and-parameters) + - [1. Alignment](#1-alignment) + - [2. QC stats from the alignment files](#2-qc-stats-from-the-alignment-files) + - [3. Repeat expansions](#3-repeat-expansions) + - [4. Variant calling - SNV](#4-variant-calling---snv) + - [5. Variant calling - Structural variants](#5-variant-calling---structural-variants) + - [6. Copy number variant calling](#6-copy-number-variant-calling) + - [7. SNV annotation \& Ranking](#7-snv-annotation--ranking) + - [8. SV annotation \& Ranking](#8-sv-annotation--ranking) + - [9. Mitochondrial annotation](#9-mitochondrial-annotation) + - [10. Mobile element calling](#10-mobile-element-calling) + - [11. Mobile element annotation](#11-mobile-element-annotation) + - [12. Variant evaluation](#12-variant-evaluation) + - [13. Prepare data for CNV visualisation in Gens](#13-prepare-data-for-cnv-visualisation-in-gens) + - [Run the pipeline](#run-the-pipeline) + - [Direct input in CLI](#direct-input-in-cli) + - [Import from a config file (recommended)](#import-from-a-config-file-recommended) - [Best practices](#best-practices) - [Core Nextflow arguments](#core-nextflow-arguments) - [`-profile`](#-profile)