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)