Merge pull request #61 from Ferlab-Ste-Justine/feat/ensemblvep-download

Feat/ensemblvep download

CHANGELOG.md

@@ -3,7 +3,15 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v2.4.1-dev - [date]
+## Unreleased 
+
+### `Added`
+- [#61](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/61) Add download VEP module form nf-core
+
+### `Changed`
+- [#59](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/59) Add ".snv" to VEP output filename prefix
+
+## v2.4.1-dev - 16/01/2025
 
 ## v2.4.0-dev
 
@@ -26,7 +34,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 - [#54](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/54) Standardize exomiser output filenames
-- [#59](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/59) Add ".snv" to VEP output filename prefix
 
 ### `Fixed`
 - [#50](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/50) Use container tag 1.20 for splitMultiAllelics process

README.md

@@ -22,7 +22,7 @@ It performs joint genotyping, tags low-quality variants, and optionally annotate
 6. Tag false positive variants with either:
   - For whole genome sequencing data: [Variant quality score recalibration (VQSR)](https://gatk.broadinstitute.org/hc/en-us/articles/360036510892-VariantRecalibrator)
   - For whole exome sequencing data: [Hard-Filtering](https://gatk.broadinstitute.org/hc/en-us/articles/360036733451-VariantFiltration)
-7. Optionnally annotate variants with [Variant effect predictor (VEP)](https://useast.ensembl.org/info/docs/tools/vep/index.html)
+7. Optionnally annotate variants with [Variant effect predictor (VEP)](https://useast.ensembl.org/info/docs/tools/vep/index.html) and download reference cache (if not provided)
 8. Optionnally integrate phenotype data to annotate, filter and prioritise variants likely to be disease-causing with [exomiser](https://www.sanger.ac.uk/tool/exomiser/)
 
 
@@ -76,7 +76,7 @@ See [docs/output.md](docs/output.md) for more details about pipeline outputs.
 
 ## Credits
 
-Ferlab-Ste-Justine/Post-processing-Pipeline was originally written by Damien Geneste, David Morais, Felix-Antoine Le Sieur, Jeremy Costanza, Lysiane Bouchard.
+Ferlab-Ste-Justine/Post-processing-Pipeline was originally written by Damien Geneste, David Morais, Felix-Antoine Le Sieur, Jeremy Costanza, Lysiane Bouchard, Georgette Femerling.
 
 
 ## Contributions and Support

conf/modules.config

@@ -71,6 +71,18 @@ process {
         ext.args = { "--output-filename=${meta.id}.exomiser" }
     }
 
+    withName: ENSEMBLVEP_DOWNLOAD {
+        // Using the conda container as the official one from esemblorg does not have the download_vep function used in nf-core. 
+        container = 'quay.io/biocontainers/ensembl-vep:111.0--pl5321h2a3209d_0' 
+        ext.when  = { params.tools && (params.tools.split(',').contains('vep')) }
+        ext.args  = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE'
+        ext.prefix  = { "${params.vep_cache_version}_${params.vep_genome}" }
+        publishDir  = [
+            mode: params.publish_dir_mode,
+            path: { params.outdir_cache ? "${params.outdir_cache}/": "${params.outdir}/cache/" }
+        ]
+    }
+
     withName: ENSEMBLVEP_VEP {
         container = 'ensemblorg/ensembl-vep:release_111.0' //sticking to v111 for now, but we should update this
         def args_list =  [

docs/reference_data.md

@@ -46,7 +46,7 @@ For more details, see [Gatk documentation](https://gatk.broadinstitute.org/hc/en
 
 
 ## VEP Cache Directory
-The `vepCache` parameter specifies the directory for the vep cache. It is only required if `vep` is specified via the
+The `vep_cache` parameter specifies the directory for the vep cache. It is only required if `vep` is specified via the
 `tools` parameter.
 
 The vep cache is not automatically populated by the pipeline. It must be pre-downloaded. You can obtain a copy of the 

docs/usage.md

@@ -194,7 +194,11 @@ Parameters summary
 | `broad` | _Optional_ | Path to the directory containing Broad reference data (for VQSR) |
 | `intervalsFile` | _Optional_ | Path to the file containg the genome intervals list on which to operate |
 | `tools` | _Optional_ | Additional tools to run separated by commas. Supported tools are `vep` and `exomiser` |
-| `vepCache` | _Optional_ | Path to the vep cache data directory |
+| `vep_cache` | _Optional_ | Path to the vep cache data directory |
+| `vep_cache_version` | _Optional_ | Version of the vep cache. e.g. `111` |
+| `vep_genome` | _Optional_ | Genome assembly version of the vep cache  |
+| `download_cache` | _Optional_ | Download vep cache (default: false) |
+| `outdir_cache` | _Optional_ |  Path to write the cache to. If not declared, cache will be written to `<outputdir>/cache/` |
 | `exclude_mnps` | _Optional_ | Replace MNPs by individual SNPs (default: true). Must be true on whole genome data. |
 | `exomiser_data_dir` | _Optional_ | Path to the exomiser reference data directory |
 | `exomiser_genome` | _Optional_ | Genome assembly version to be used by exomiser(`hg19` or `hg38`) |

modules.json

@@ -20,6 +20,11 @@
             "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
             "installed_by": ["modules"]
           },
+          "ensemblvep/download": {
+            "branch": "master",
+            "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
+            "installed_by": ["modules"]
+          },
           "ensemblvep/vep": {
             "branch": "master",
             "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",