Merge pull request #143 from MaxUlysse/FixAnnotationCI

fix annotation tests
nf-core · Mar 5, 2020 · ee4f5b0 · ee4f5b0
2 parents dd2a0ac + 456dd79
commit ee4f5b0
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Showing 7 changed files with 19 additions and 18 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -5,7 +5,7 @@ jobs:
       - image: circleci/buildpack-deps:stretch
     environment:
       GENOME: GRCh37
-      SNPEFF_CACHE_VERSION: "87"
+      SNPEFF_CACHE_VERSION: "75"
     steps:
       - checkout
       - setup_remote_docker
@@ -20,7 +20,7 @@ jobs:
     << : *buildsnpeff
     environment:
       GENOME: GRCh38
-      SNPEFF_CACHE_VERSION: "92"
+      SNPEFF_CACHE_VERSION: "86"
 
   snpeffgrcm38:
     << : *buildsnpeff
@@ -60,29 +60,24 @@ jobs:
     << : *buildvep
     environment:
       GENOME: GRCh38
-      SPECIES: homo_sapiens
-      VEP_VERSION: "99"
 
   vepgrcm38:
     << : *buildvep
     environment:
       GENOME: GRCm38
       SPECIES: mus_musculus
-      VEP_VERSION: "99"
 
   vepcanfam3_1:
     << : *buildvep
     environment:
       GENOME: CanFam3.1
       SPECIES: canis_familiaris
-      VEP_VERSION: "99"
 
   vepwbcel235:
     << : *buildvep
     environment:
       GENOME: WBcel235
       SPECIES: caenorhabditis_elegans
-      VEP_VERSION: "99"
 
 workflows:
   version: 2

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -32,7 +32,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        tools: [snpeff, VEP]
+        tools: [snpeff, vep]
         species: [WBcel235]
     steps:
       - uses: actions/checkout@v2

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -37,6 +37,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#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`
+- [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `75` for `GRCh37`
+- [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `86` for `GRCh38`
 
 ### `Fixed`
 
@@ -50,6 +52,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#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`
+- [#143](https://github.com/nf-core/sarek/pull/143) - Fix annotation CI testing with `snpEff` and `VEP`
 
 ### `Deprecated`
 

diff --git a/conf/genomes.config b/conf/genomes.config
@@ -25,7 +25,7 @@ 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      = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
-      snpeff_db               = 'GRCh37.87'
+      snpeff_db               = 'GRCh37.75'
       species                 = 'homo_sapiens'
       vep_cache_version       = '99'
     }
@@ -45,7 +45,7 @@ params {
       intervals               = "${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               = 'GRCh38.92'
+      snpeff_db               = 'GRCh38.86'
       species                 = 'homo_sapiens'
       vep_cache_version       = '99'
     }
@@ -66,5 +66,10 @@ params {
       fasta                   = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
       known_indels            = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
     }
+    'WBcel235' {
+      snpeff_db               = 'WBcel235.86'
+      species                 = 'caenorhabditis_elegans'
+      vep_cache_version       = '99'
+    }
   }
 }
diff --git a/conf/igenomes.config b/conf/igenomes.config
@@ -25,7 +25,7 @@ params {
       intervals               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/intervals/wgs_calling_regions_Sarek.list"
       known_indels            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
       known_indels_index      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
-      snpeff_db               = 'GRCh37.87'
+      snpeff_db               = 'GRCh37.75'
       species                 = 'homo_sapiens'
       vep_cache_version       = '99'
     }
@@ -45,7 +45,7 @@ params {
       intervals               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions.hg38.bed"
       known_indels            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
       known_indels_index      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
-      snpeff_db               = 'GRCh38.92'
+      snpeff_db               = 'GRCh38.86'
       species                 = 'homo_sapiens'
       vep_cache_version       = '99'
     }
@@ -84,6 +84,9 @@ params {
     'WBcel235' {
       bwa                     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
       fasta                   = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
+      snpeff_db               = 'WBcel235.86'
+      species                 = 'caenorhabditis_elegans'
+      vep_cache_version       = '99'
     }
     'ce10' {
       bwa                     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"

diff --git a/conf/test_annotation.config b/conf/test_annotation.config
@@ -10,9 +10,6 @@
 includeConfig 'test.config'
 
 params {
-  input             = 'https://github.com/nf-core/test-datasets/raw/sarek/testdata/vcf/Strelka_1234N_variants.vcf.gz'
   genome            = 'WBcel235'
-  species           = 'caenorhabditis_elegans'
-  vep_cache_version = '99'
-  snpeff_db         = 'WBcel235.86'
+  input             = 'https://github.com/nf-core/test-datasets/raw/sarek/testdata/vcf/Strelka_1234N_variants.vcf.gz'
 }
diff --git a/main.nf b/main.nf
@@ -418,8 +418,6 @@ if (tsvPath) {
 
 (genderMap, statusMap, inputSample) = extractInfos(inputSample)
 
-
-
 /*
 ================================================================================
                                CHECKING REFERENCES
-Original file line number
+Diff line change
@@ Expand Up / @@ -418,8 +418,6 @@ if (tsvPath) { @@
     (genderMap, statusMap, inputSample) = extractInfos(inputSample)
     /*
     ================================================================================
                                    CHECKING REFERENCES
@@ Expand Down @@