Merge pull request #1656 from asp8200/modify_snpeff_cache_setup

Retire snpeff_genome
nf-core · Sep 23, 2024 · a4f07f7 · a4f07f7
2 parents 163823c + 9e3356a
commit a4f07f7
Show file tree

Hide file tree

Showing 18 changed files with 201 additions and 58 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,14 +9,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-- [1640](https://github.com/nf-core/sarek/pull/1620) - Add `lofreq` as a tumor-only variant caller.
+- [1640](https://github.com/nf-core/sarek/pull/1620) - Add `lofreq` as a tumor-only variant caller
 - [1642](https://github.com/nf-core/sarek/pull/1642) - Back to dev
 - [1660](https://github.com/nf-core/sarek/pull/1642) - Add `--length_required` for minimal reads length with `FASTP`
 
 ### Changed
 
 ### Fixed
 
+- [1656](https://github.com/nf-core/sarek/pull/1656) - Retiring parameter `snpeff_genome`
 - [1657](https://github.com/nf-core/sarek/pull/1657) - Update all actions used in the GHA CI
 
 ### Removed

diff --git a/conf/igenomes.config b/conf/igenomes.config
@@ -36,8 +36,7 @@ params {
             known_indels_vqsr     = '--resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_phase1.indels.b37.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.b37.vcf.gz'
             mappability           = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem"
             ngscheckmate_bed      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/NGSCheckMate/SNP_GRCh37_hg19_woChr.bed"
-            snpeff_db             = '87'
-            snpeff_genome         = 'GRCh37'
+            snpeff_db             = 'GRCh37.87'
             vep_cache_version     = '111'
             vep_genome            = 'GRCh37'
             vep_species           = 'homo_sapiens'
@@ -73,8 +72,7 @@ params {
             pon                     = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz"
             pon_tbi                 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi"
             sentieon_dnascope_model = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model"
-            snpeff_db               = '105'
-            snpeff_genome           = 'GRCh38'
+            snpeff_db               = 'GRCh38.105'
             vep_cache_version       = '111'
             vep_genome              = 'GRCh38'
             vep_species             = 'homo_sapiens'
@@ -84,8 +82,7 @@ params {
             fasta                 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
             ngscheckmate_bed      = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/NGSCheckMate/SNP_GRCh37_hg19_woChr.bed"
             readme                = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
-            snpeff_db             = '87'
-            snpeff_genome         = 'GRCh37'
+            snpeff_db             = 'GRCh37.87'
             vep_cache_version     = '111'
             vep_genome            = 'GRCh37'
             vep_species           = 'homo_sapiens'
@@ -94,8 +91,7 @@ params {
             bwa                   = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
             fasta                 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
             ngscheckmate_bed      ="${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed"
-            snpeff_db             = '105'
-            snpeff_genome         = 'GRCh38'
+            snpeff_db             = 'GRCh38.105'
             vep_cache_version     = '111'
             vep_genome            = 'GRCh38'
             vep_species           = 'homo_sapiens'
@@ -118,8 +114,7 @@ params {
             known_indels_tbi      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi"
             mappability           = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Control-FREEC/GRCm38_68_mm10.gem"
             readme                = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
-            snpeff_db             = '99'
-            snpeff_genome         = 'GRCm38'
+            snpeff_db             = 'GRCm38.99'
             vep_cache_version     = '102'
             vep_genome            = 'GRCm38'
             vep_species           = 'mus_musculus'
@@ -138,17 +133,15 @@ params {
             bwa                   = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
             fasta                 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
             readme                = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
-            snpeff_db             = '75'
-            snpeff_genome         = 'UMD3.1'
+            snpeff_db             = 'UMD3.1.75'
             vep_cache_version     = '94'
             vep_genome            = 'UMD3.1'
             vep_species           = 'bos_taurus'
         }
         'WBcel235' {
             bwa                   = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
             fasta                 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
-            snpeff_db             = '105'
-            snpeff_genome         = 'WBcel235'
+            snpeff_db             = 'WBcel235.105'
             vep_cache_version     = '111'
             vep_genome            = 'WBcel235'
             vep_species           = 'caenorhabditis_elegans'
@@ -157,8 +150,7 @@ params {
             bwa                   = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
             fasta                 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
             readme                = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
-            snpeff_db             = '99'
-            snpeff_genome         = 'CanFam3.1'
+            snpeff_db             = 'CanFam3.1.99'
             vep_cache_version     = '104'
             vep_genome            = 'CanFam3.1'
             vep_species           = 'canis_lupus_familiaris'
@@ -215,8 +207,7 @@ params {
         'R64-1-1' {
             bwa                   = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
             fasta                 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
-            snpeff_db             = '105'
-            snpeff_genome         = 'R64-1-1'
+            snpeff_db             = 'R64-1-1.105'
             vep_cache_version     = '111'
             vep_genome            = 'R64-1-1'
             vep_species           = 'saccharomyces_cerevisiae'
@@ -243,8 +234,7 @@ params {
         'hg38' {
             bwa                   = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
             fasta                 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
-            snpeff_db             = '105'
-            snpeff_genome         = 'GRCh38'
+            snpeff_db             = 'GRCh38.105'
             vep_cache_version     = '111'
             vep_genome            = 'GRCh38'
             vep_species           = 'homo_sapiens'
@@ -253,8 +243,7 @@ params {
             bwa                   = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
             fasta                 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
             readme                = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
-            snpeff_db             = '87'
-            snpeff_genome         = 'GRCh37'
+            snpeff_db             = 'GRCh37.87'
             vep_cache_version     = '111'
             vep_genome            = 'GRCh37'
             vep_species           = 'homo_sapiens'
@@ -263,8 +252,7 @@ params {
             bwa                   = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
             fasta                 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
             readme                = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
-            snpeff_db             = '99'
-            snpeff_genome         = 'GRCm38'
+            snpeff_db             = 'GRCm38.99'
             vep_cache_version     = '102'
             vep_genome            = 'GRCm38'
             vep_species           = 'mus_musculus'
@@ -334,8 +322,7 @@ params {
             known_indels_tbi        = "${params.igenomes_base}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
             known_indels_vqsr       = '--resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz'
             ngscheckmate_bed        = "${params.igenomes_base}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
-            snpeff_db               = '105'
-            snpeff_genome           = 'WBcel235'
+            snpeff_db               = 'WBcel235.105'
             vep_cache_version       = '111'
             vep_genome              = 'WBcel235'
             vep_species             = 'caenorhabditis_elegans'

diff --git a/docs/usage.md b/docs/usage.md
@@ -898,16 +898,14 @@ By default all is specified in the [igenomes.config](https://github.com/nf-core/
 Explanation can be found for all params in the documentation:
 
 - [snpeff_db](https://nf-co.re/sarek/parameters#snpeff_db)
-- [snpeff_genome](https://nf-co.re/sarek/parameters#snpeff_genome)
 - [vep_genome](https://nf-co.re/sarek/parameters#vep_genome)
 - [vep_species](https://nf-co.re/sarek/parameters#vep_species)
 - [vep_cache_version](https://nf-co.re/sarek/parameters#vep_cache_version)
 
 With the previous example of `GRCh38`, these are the values that were used for these params:
 
 ```bash
-snpeff_db         = '105'
-snpeff_genome     = 'GRCh38'
+snpeff_db         = 'GRCh38.105'
 vep_cache_version = '110'
 vep_genome        = 'GRCh38'
 vep_species       = 'homo_sapiens'
@@ -1014,6 +1012,12 @@ This command could be used to point to the recently downloaded cache and run Snp
 nextflow run nf-core/sarek --outdir results --vep_cache /path_to/my-own-cache/vep_cache --snpeff_cache /path_to/my-own-cache/snpeff_cache --tools vep,snpeff --input samplesheet_vcf.csv
 ```
 
+Here is an example on how sarek may be used to download the SnpEff cache for Candida auris:
+
+```bash
+nextflow run nf-core/sarek --outdir results --outdir_cache /path_to/my-own-cache --tools snpeff --download_cache --build_only_index --input false --snpeff_db _candida_auris_gca_001189475 --step annotate --genome null --igenomes_ignore
+```
+
 ### Create containers with pre-downloaded cache
 
 nf-core is no longer maintaining containers with pre-downloaded cache. Hosting the cache within the container is not recommended as it can cause a number of problems. Instead we recommned using an external cache. The following is left for legacy reasons.

diff --git a/main.nf b/main.nf
@@ -56,7 +56,6 @@ params.pon                     = getGenomeAttribute('pon')
 params.pon_tbi                 = getGenomeAttribute('pon_tbi')
 params.sentieon_dnascope_model = getGenomeAttribute('sentieon_dnascope_model')
 params.snpeff_db               = getGenomeAttribute('snpeff_db')
-params.snpeff_genome           = getGenomeAttribute('snpeff_genome')
 params.vep_cache_version       = getGenomeAttribute('vep_cache_version')
 params.vep_genome              = getGenomeAttribute('vep_genome')
 params.vep_species             = getGenomeAttribute('vep_species')
@@ -235,7 +234,7 @@ workflow NFCORE_SAREK {
     if (params.download_cache) {
         // Assuming that even if the cache is provided, if the user specify download_cache, sarek will download the cache
         ensemblvep_info = Channel.of([ [ id:"${params.vep_cache_version}_${params.vep_genome}" ], params.vep_genome, params.vep_species, params.vep_cache_version ])
-        snpeff_info     = Channel.of([ [ id:"${params.snpeff_genome}.${params.snpeff_db}" ], params.snpeff_genome, params.snpeff_db ])
+        snpeff_info     = Channel.of([ [ id:"${params.snpeff_db}" ], params.snpeff_db ])
         DOWNLOAD_CACHE_SNPEFF_VEP(ensemblvep_info, snpeff_info)
         snpeff_cache = DOWNLOAD_CACHE_SNPEFF_VEP.out.snpeff_cache
         vep_cache    = DOWNLOAD_CACHE_SNPEFF_VEP.out.ensemblvep_cache.map{ meta, cache -> [ cache ] }
@@ -246,7 +245,6 @@ workflow NFCORE_SAREK {
         ANNOTATION_CACHE_INITIALISATION(
             (params.snpeff_cache && params.tools && (params.tools.split(',').contains("snpeff") || params.tools.split(',').contains('merge'))),
             params.snpeff_cache,
-            params.snpeff_genome,
             params.snpeff_db,
             (params.vep_cache && params.tools && (params.tools.split(',').contains("vep") || params.tools.split(',').contains('merge'))),
             params.vep_cache,

diff --git a/modules.json b/modules.json
@@ -446,12 +446,12 @@
                     },
                     "snpeff/download": {
                         "branch": "master",
-                        "git_sha": "214d575774c172062924ad3564b4f66655600730",
+                        "git_sha": "bb8b9216efd4a578bd3c47505bafc10869d6271d",
                         "installed_by": ["modules"]
                     },
                     "snpeff/snpeff": {
                         "branch": "master",
-                        "git_sha": "2f3db6f45147ebbb56b371536e31bdf622b5bfee",
+                        "git_sha": "bb8b9216efd4a578bd3c47505bafc10869d6271d",
                         "installed_by": ["modules", "vcf_annotate_snpeff"]
                     },
                     "spring/decompress": {

diff --git a/modules/nf-core/snpeff/download/environment.yml b/modules/nf-core/snpeff/download/environment.yml
diff --git a/modules/nf-core/snpeff/download/main.nf b/modules/nf-core/snpeff/download/main.nf
diff --git a/modules/nf-core/snpeff/download/tests/main.nf.test b/modules/nf-core/snpeff/download/tests/main.nf.test