fix download cache script + further improvements

.circleci/config.yml

@@ -5,7 +5,7 @@ jobs:
       - image: circleci/buildpack-deps:stretch
     environment:
       GENOME: GRCh37
-      SNPEFF_CACHE_VERSION: "75"
+      SNPEFF_CACHE_VERSION: "87"
     steps:
       - checkout
       - setup_remote_docker
@@ -20,7 +20,7 @@ jobs:
     << : *buildsnpeff
     environment:
       GENOME: GRCh38
-      SNPEFF_CACHE_VERSION: "86"
+      SNPEFF_CACHE_VERSION: "92"
 
   snpeffgrcm38:
     << : *buildsnpeff
@@ -34,13 +34,19 @@ jobs:
       GENOME: CanFam3.1
       SNPEFF_CACHE_VERSION: "86"
 
+  snpeffwbcel235:
+    << : *buildsnpeff
+    environment:
+      GENOME: WBcel235
+      SNPEFF_CACHE_VERSION: "86"
+
   vepgrch37: &buildvep
     docker:
       - image: circleci/buildpack-deps:stretch
     environment:
       GENOME: GRCh37
       SPECIES: homo_sapiens
-      VEP_VERSION: "95"
+      VEP_VERSION: "99"
     steps:
       - checkout
       - setup_remote_docker
@@ -55,21 +61,28 @@ jobs:
     environment:
       GENOME: GRCh38
       SPECIES: homo_sapiens
-      VEP_VERSION: "95"
+      VEP_VERSION: "99"
 
   vepgrcm38:
     << : *buildvep
     environment:
       GENOME: GRCm38
       SPECIES: mus_musculus
-      VEP_VERSION: "95"
+      VEP_VERSION: "99"
 
   vepcanfam3_1:
     << : *buildvep
     environment:
       GENOME: CanFam3.1
       SPECIES: canis_familiaris
-      VEP_VERSION: "95"
+      VEP_VERSION: "99"
+
+  vepwbcel235:
+    << : *buildvep
+    environment:
+      GENOME: WBcel235
+      SPECIES: caenorhabditis_elegans
+      VEP_VERSION: "99"
 
 workflows:
   version: 2
@@ -79,7 +92,9 @@ workflows:
       - snpeffgrch37
       - snpeffgrch38
       - snpeffgrcm38
+      - snpeffwbcel235
       - vepcanfam3_1
       - vepgrch37
       - vepgrch38
       - vepgrcm38
+      - vepwbcel235

.github/workflows/ci.yml

@@ -32,8 +32,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        tools: [snpeff]
-        species: [GRCh37]
+        tools: [snpeff, VEP]
+        species: [WBcel235]
     steps:
       - uses: actions/checkout@v2
       - name: Install Nextflow

CHANGELOG.md

@@ -12,6 +12,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#87](https://github.com/nf-core/sarek/pull/87) - Add `GATK BaseRecalibrator` plot to `MultiQC` report
 - [#115](https://github.com/nf-core/sarek/pull/115) - Add [@szilvajuhos](https://github.com/szilvajuhos) abstract for ESHG2020
 - [#117](https://github.com/nf-core/sarek/pull/117) - Add `Trim Galore` possibilities to Sarek
+- [#141](https://github.com/nf-core/sarek/pull/141) - Add containers for `WBcel235`
 
 ### `Changed`
 
@@ -33,6 +34,9 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#131](https://github.com/nf-core/sarek/pull/131) - Update `Manta` to `1.6.0`
 - [#131](https://github.com/nf-core/sarek/pull/131) - Update `Qualimap` to `2.2.2d`
 - [#131](https://github.com/nf-core/sarek/pull/131) - Update `VEP` to `99.2`
+- [#141](https://github.com/nf-core/sarek/pull/141) - Update `snpEff` cache version to `87` for `GRCh37`
+- [#141](https://github.com/nf-core/sarek/pull/141) - Update `snpEff` cache version to `92` for `GRCh38`
+- [#141](https://github.com/nf-core/sarek/pull/141) - Update `VEP` databases to `99`
 
 ### `Fixed`
 
@@ -41,10 +45,11 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#110](https://github.com/nf-core/sarek/pull/110) - Fix `snpEff` report issue cf [#106](https://github.com/nf-core/sarek/issues/106)
 - [#126](https://github.com/nf-core/sarek/pull/126) - Fix `iGenomes` paths
 - [#127](https://github.com/nf-core/sarek/pull/127), [#128](https://github.com/nf-core/sarek/pull/128) - Fix `ASCAT`
-- [#129](https://github.com/nf-core/sarek/pull/129)- Fix issue with Channel `channel ch_software_versions_yaml`
-- [#129](https://github.com/nf-core/sarek/pull/129)- Apply @drpatelh fix for `mardown_to_html.py` compatibility with Python 2
-- [#129](https://github.com/nf-core/sarek/pull/129)- Removed `Python` `3.7.3` from conda environment due to incompatibility
-- [#129](https://github.com/nf-core/sarek/pull/129)- Change ascii characters that were not supported from the `output.md` docs
+- [#129](https://github.com/nf-core/sarek/pull/129) - Fix issue with Channel `channel ch_software_versions_yaml`
+- [#129](https://github.com/nf-core/sarek/pull/129) - Apply @drpatelh fix for `mardown_to_html.py` compatibility with Python 2
+- [#129](https://github.com/nf-core/sarek/pull/129) - Removed `Python` `3.7.3` from conda environment due to incompatibility
+- [#129](https://github.com/nf-core/sarek/pull/129) - Change ascii characters that were not supported from the `output.md` docs
+- [#141](https://github.com/nf-core/sarek/pull/141) - Fix `download_cache.nf` script to download cache for `snpEff` and `VEP`
 
 ### `Deprecated`
 

conf/genomes.config

@@ -25,9 +25,9 @@ params {
       intervals               = "${params.genomes_base}/wgs_calling_regions_Sarek.list"
       known_indels            = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
       known_indels_index      = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
-      snpeff_db               = 'GRCh37.75'
+      snpeff_db               = 'GRCh37.87'
       species                 = 'homo_sapiens'
-      vep_cache_version       = '95'
+      vep_cache_version       = '99'
     }
     'GRCh38' {
       ac_loci                 = "${params.genomes_base}/1000G_phase3_GRCh38_maf0.3.loci"
@@ -45,9 +45,9 @@ params {
       intervals               = "${params.genomes_base}/wgs_calling_regions.hg38.bed"
       known_indels            = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
       known_indels_index      = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
-      snpeff_db               = 'GRCh38.86'
+      snpeff_db               = 'GRCh38.92'
       species                 = 'homo_sapiens'
-      vep_cache_version       = '95'
+      vep_cache_version       = '99'
     }
     'minimalGRCh37' {
       fasta                   = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
@@ -58,9 +58,9 @@ params {
       germline_resource       = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
       intervals               = "${params.genomes_base}/small.intervals"
       known_indels            = "${params.genomes_base}/Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz"
-      snpeff_db               = 'GRCh37.75'
+      snpeff_db               = 'GRCh37.87'
       species                 = 'homo_sapiens'
-      vep_cache_version       = '95'
+      vep_cache_version       = '99'
     }
     'smallerGRCh37' {
       fasta                   = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"