Fix file requirements (#317)

* Split vep plugins into vep cache and vep plugins

* Fix file requirements

CHANGELOG.md

@@ -62,6 +62,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#312](https://github.com/genomic-medicine-sweden/nallo/pull/312) - Changed echtvar encode database creation to use dynamic `${project}` from samplesheet
 - [#313](https://github.com/genomic-medicine-sweden/nallo/pull/313) - Updated calling of variants in non-autosomal contigs for DeepVariant
 - [#314](https://github.com/genomic-medicine-sweden/nallo/pull/314) - Changed VEP annotation added in #244 to not include SpliceAI
+- [#317](https://github.com/genomic-medicine-sweden/nallo/pull/317) - Changed so that `--reduced_penetrance` and `--score_config_snv` is required by rank variants and not SNV annotation
 - [#321](https://github.com/genomic-medicine-sweden/nallo/pull/321) - Changed the input to BUILD_INTERVALS to have `meta.id` when building intervals from reference
 
 ### `Removed`

docs/usage.md

@@ -112,8 +112,11 @@ Some workflows require additional files:
 - If running without `--skip_repeat_annotation`, download a json variant catalog, (e.g. [variant_catalog_grch38.json](https://github.com/Clinical-Genomics/stranger/raw/main/stranger/resources/variant_catalog_grch38.json)) matching your reference genome to supply with `--variant_catalog`.
 
 - If running without `--skip_snv_annotation`, download [VEP cache](https://ftp.ensembl.org/pub/release-110/variation/vep/homo_sapiens_vep_110_GRCh38.tar.gz) to supply with `--vep_cache` and prepare a samplesheet with annotation databases ([`echtvar encode`](https://github.com/brentp/echtvar)) to supply with `--snp_db`:
+
 - If running without `--skip_snv_annotation`, you will also need to download VEP plugin files to supply with `--vep_plugin_files` see [example](https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugin_files.csv). PLI and LoFtool.
 
+- If running without `--skip_snv_annotation`, `--variant_consequences_snv` is also required (File 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)).
+
 ```
 vep_files
 https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo/reference/vep_plugins/SpliceAI.pm
@@ -136,7 +139,7 @@ gnomad,/path/to/gnomad.v3.1.2.echtvar.popmax.v2.zip
 cadd,/path/to/cadd.v1.6.hg38.zip
 ```
 
-- If your samplesheet contains at least one affected sample (phenotype = 2), `--reduced_penetrance` (Used 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)), `--score_config_snv` (Used by GENMOD for ranking the variants. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/rank_model_snv.ini)) and `--variant_consequences_snv` (File 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)) is also required.
+- If running wihtout `--skip_rank_variants` and your samplesheet contains at least one affected sample (phenotype = 2), `--reduced_penetrance` (Used 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)), `--score_config_snv` (Used by GENMOD for ranking the variants. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/rank_model_snv.ini)).
 
 - Optionally, if running without `--skip_snv_annotation`, supply a path to a folder containing cadd annotations with `--cadd_resources` and prescored indels with `--cadd_prescored`. Equivalent of the data/annotations/ and data/prescored/ folders described [here](https://github.com/kircherlab/CADD-scripts/#manual-installation), and it is used to calculate CADD scores for small indels.
 

subworkflows/local/utils_nfcore_nallo_pipeline/main.nf

@@ -74,8 +74,9 @@ def fileDependencies = [
     mapping          : ["fasta", "somalier_sites"],
     assembly         : ["fasta", "par_regions"], // The assembly workflow should be split into two - assembly and variant calling (requires ref)
     snv_calling      : ["fasta", "par_regions"],
-    snv_annotation   : ["snp_db", "vep_cache", "vep_plugin_files", "reduced_penetrance", "score_config_snv", "variant_consequences_snv"],
+    snv_annotation   : ["snp_db", "vep_cache", "vep_plugin_files", "variant_consequences_snv"],
     cnv_calling      : ["hificnv_xy", "hificnv_xx", "hificnv_exclude"],
+    rank_variants    : ["reduced_penetrance", "score_config_snv"],
     repeat_calling   : ["trgt_repeats"],
     repeat_annotation: ["variant_catalog"],
 ]