Merge ef11ce7 into 800bd37

Clinical-Genomics · Apr 23, 2020 · 4f6cb60 · 4f6cb60
2 parents 800bd37 + ef11ce7
commit 4f6cb60
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Showing 24 changed files with 29 additions and 26 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,13 +22,15 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - picard: 2.20.7 -> 2.22.0 (DNA)
 - samtools: 1.9=h8571acd_11 -> 1.10-h9402c20_2 (DNA)
 - SMNCopyNumberCaller: 4b2c1ad -> 1.0
+- VEP: 97 -> 99
 
 **References**
 - grch38_frequency_vcfanno_filter_config_-v1.2-.toml -> grch38_frequency_vcfanno_filter_config_-v1.3-.toml
 - grch37_frequency_vcfanno_filter_config_-v1.3-.toml -> grch37_frequency_vcfanno_filter_config_-v1.4-.toml
 - grch37_frequency_vcfanno_filter_config_-v1.3-.toml -> grch37_frequency_vcfanno_filter_config_-v1.5-.toml
 - grch37_loqusdb_snv_indel_-2019-11-04-.vcf.gz -> grch37_loqusdb_snv_indel_-2020-03-24-.vcf.gz
 - grch37_loqusdb_sv_-2020-04-20.vcf
+- VEP cache: 97 -> 99
 
 ## [8.2.4]
 - Chromograph patch

diff --git a/t/check_vep_api_cache_versions.t b/t/check_vep_api_cache_versions.t
@@ -25,7 +25,7 @@ use MIP::Constants qw{ $COMMA $SPACE };
 use MIP::Test::Fixtures qw{ test_log test_standard_cli };
 
 my $VERBOSE = 1;
-our $VERSION = 1.04;
+our $VERSION = 1.05;
 
 $VERBOSE = test_standard_cli(
     {
@@ -67,7 +67,8 @@ my $log = test_log( {} );
 ## Given matching vep API and cache version
 my $vep_binary_path =
   catdir( $Bin, qw{ data modules miniconda envs mip_travis bin vep } );
-my $vep_directory_cache = catdir( $Bin, qw{ data references ensembl-tools-data cache } );
+my $vep_directory_cache =
+  catdir( $Bin, qw{ data references ensembl-tools-data-99 cache } );
 
 ## When comparing API and cache version
 my $match = check_vep_api_cache_versions(
@@ -81,7 +82,7 @@ my $match = check_vep_api_cache_versions(
 ok( $match, q{Return on matching versions} );
 
 ## Given non matching API and cache
-$vep_directory_cache = catdir( $Bin, qw{ data references ensembl-tools-data cache2 } );
+$vep_directory_cache = catdir( $Bin, qw{ data references ensembl-tools-data-99 cache2 } );
 
 ## When comparing API and cache version
 trap {

diff --git a/...bl-tools-97/cache/cache/Plugins/Hello.txt → ...bl-tools-99/cache/cache/Plugins/Hello.txt b/...bl-tools-97/cache/cache/Plugins/Hello.txt → ...bl-tools-99/cache/cache/Plugins/Hello.txt
diff --git a/...cache/Plugins/fordownload/Hello_world.txt → ...cache/Plugins/fordownload/Hello_world.txt b/...cache/Plugins/fordownload/Hello_world.txt → ...cache/Plugins/fordownload/Hello_world.txt
diff --git a/...-97/cache/cache/Plugins/human_ancestor.fa → ...-99/cache/cache/Plugins/human_ancestor.fa b/...-97/cache/cache/Plugins/human_ancestor.fa → ...-99/cache/cache/Plugins/human_ancestor.fa
diff --git a/...nsembl-tools-data/cache/Plugins/Hello.txt → ...mbl-tools-data-99/cache/Plugins/Hello.txt b/...nsembl-tools-data/cache/Plugins/Hello.txt → ...mbl-tools-data-99/cache/Plugins/Hello.txt
diff --git a/...ols-data/cache/Plugins/LoFtool_scores.txt → ...-data-99/cache/Plugins/LoFtool_scores.txt b/...ols-data/cache/Plugins/LoFtool_scores.txt → ...-data-99/cache/Plugins/LoFtool_scores.txt
diff --git a/...cache/Plugins/fordownload/Hello_world.txt → ...cache/Plugins/fordownload/Hello_world.txt b/...cache/Plugins/fordownload/Hello_world.txt → ...cache/Plugins/fordownload/Hello_world.txt
diff --git a/...ools-data/cache/Plugins/human_ancestor.fa → ...s-data-99/cache/Plugins/human_ancestor.fa b/...ools-data/cache/Plugins/human_ancestor.fa → ...s-data-99/cache/Plugins/human_ancestor.fa
diff --git a/...ta/cache/homo_sapiens/95_GRCh37/Hello.txt → ...99/cache/homo_sapiens/95_GRCh37/Hello.txt b/...ta/cache/homo_sapiens/95_GRCh37/Hello.txt → ...99/cache/homo_sapiens/95_GRCh37/Hello.txt
diff --git a/...ta/cache/homo_sapiens/97_GRCh37/Hello.txt → ...99/cache/homo_sapiens/97_GRCh37/Hello.txt b/...ta/cache/homo_sapiens/97_GRCh37/Hello.txt → ...99/cache/homo_sapiens/97_GRCh37/Hello.txt
diff --git a/...e/homo_sapiens_merged/95_GRCh37/Hello.txt → ...99/cache/homo_sapiens/99_GRCh37/Hello.txt b/...e/homo_sapiens_merged/95_GRCh37/Hello.txt → ...99/cache/homo_sapiens/99_GRCh37/Hello.txt
diff --git a/...e/homo_sapiens_merged/97_GRCh37/Hello.txt → ...e/homo_sapiens_merged/95_GRCh37/Hello.txt b/...e/homo_sapiens_merged/97_GRCh37/Hello.txt → ...e/homo_sapiens_merged/95_GRCh37/Hello.txt
diff --git a/...a/cache2/homo_sapiens/95_GRCh37/Hello.txt → ...e/homo_sapiens_merged/97_GRCh37/Hello.txt b/...a/cache2/homo_sapiens/95_GRCh37/Hello.txt → ...e/homo_sapiens_merged/97_GRCh37/Hello.txt
diff --git a/...2/homo_sapiens_merged/95_GRCh37/Hello.txt → ...9/cache2/homo_sapiens/95_GRCh37/Hello.txt b/...2/homo_sapiens_merged/95_GRCh37/Hello.txt → ...9/cache2/homo_sapiens/95_GRCh37/Hello.txt
diff --git a/t/data/references/ensembl-tools-data-99/cache2/homo_sapiens_merged/95_GRCh37/Hello.txt b/t/data/references/ensembl-tools-data-99/cache2/homo_sapiens_merged/95_GRCh37/Hello.txt
diff --git a/templates/grch38_mip_rd_dna_config.yaml b/templates/grch38_mip_rd_dna_config.yaml
@@ -90,8 +90,8 @@ vep_custom_annotation:
     file_type: vcf
     path: cluster_constant_path!/references/grch38_clinvar_reformated_-20190305-.vcf.gz
     vcf_fields: CLNSIG,CLNVID,CLNREVSTAT
-vep_directory_cache: cluster_constant_path!/modules/miniconda/envs/test_env/ensembl-tools-95/cache/
-vep_plugins_dir_path: cluster_constant_path!/modules/miniconda/envs/test_env/ensembl-tools-95/cache/Plugins
+vep_directory_cache: cluster_constant_path!/modules/miniconda/envs/test_env/ensembl-tools-99/cache/
+vep_plugins_dir_path: cluster_constant_path!/modules/miniconda/envs/test_env/ensembl-tools-99/cache/Plugins
 vep_plugin:
   dbNSFP:
     exists_check: file
@@ -107,10 +107,10 @@ vep_plugin:
     path: cluster_constant_path!/references/gnomad_pli_per_gene_-_r2.1.1-.txt
   LoFtool:
     exists_check: file
-    path: cluster_constant_path!/references/ensembl-tools-data/cache/Plugins/LoFtool_scores.txt
+    path: cluster_constant_path!/references/ensembl-tools-data-99/cache/Plugins/LoFtool_scores.txt
   MaxEntScan:
     exists_check: directory
     parameters:
       - SWA
       - NCSS
-    path: cluster_constant_path!/modules/miniconda/envs/test_env/ensembl-tools-95/cache/Plugin/fordownload
+    path: cluster_constant_path!/modules/miniconda/envs/test_env/ensembl-tools-99/cache/Plugin/fordownload
diff --git a/templates/mip_dragen_rd_dna_config.yaml b/templates/mip_dragen_rd_dna_config.yaml
@@ -66,8 +66,8 @@ vep_custom_annotation:
     file_type: vcf
     path: cluster_constant_path!/references/grch37_clinvar_reformated_-20190305-.vcf.gz
     vcf_fields: CLNSIG,CLNVID,CLNREVSTAT
-vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data/cache/
-vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data/cache/Plugins
+vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-99/cache/
+vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-99/cache/Plugins
 vep_plugin:
   dbNSFP:
     exists_check: file
@@ -83,10 +83,10 @@ vep_plugin:
     path: cluster_constant_path!/references/gnomad_pli_per_gene_-_r2.1.1-.txt
   LoFtool:
     exists_check: file
-    path: cluster_constant_path!/references/ensembl-tools-data/cache/Plugins/LoFtool_scores.txt
+    path: cluster_constant_path!/references/ensembl-tools-data-99/cache/Plugins/LoFtool_scores.txt
   MaxEntScan:
     exists_check: directory
     parameters:
       - SWA
       - NCSS
-    path: cluster_constant_path!/references/ensembl-tools-data/cache/Plugins/fordownload
+    path: cluster_constant_path!/references/ensembl-tools-data-99/cache/Plugins/fordownload
diff --git a/templates/mip_install_rd_dna_config_-1.0-.yaml b/templates/mip_install_rd_dna_config_-1.0-.yaml
@@ -155,7 +155,7 @@ singularity:
   vep:
     executable:
       vep:
-    uri: docker://ensemblorg/ensembl-vep:release_97.4
+    uri: docker://ensemblorg/ensembl-vep:release_99.2
   vcf2cytosure:
     executable:
       vcf2cytosure:

diff --git a/templates/mip_install_rd_rna_config_-1.0-.yaml b/templates/mip_install_rd_rna_config_-1.0-.yaml
@@ -108,4 +108,4 @@ singularity:
   vep:
     executable:
       vep:
-    uri: docker://ensemblorg/ensembl-vep:release_97.4
+    uri: docker://ensemblorg/ensembl-vep:release_99.2
diff --git a/templates/mip_rd_dna_config.yaml b/templates/mip_rd_dna_config.yaml
@@ -72,8 +72,8 @@ vep_custom_annotation:
     file_type: vcf
     path: cluster_constant_path!/references/grch37_clinvar_reformated_-20190305-.vcf.gz
     vcf_fields: CLNSIG,CLNVID,CLNREVSTAT
-vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data/cache/
-vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data/cache/Plugins
+vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-99/cache/
+vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-99/cache/Plugins
 vep_plugin:
   dbNSFP:
     exists_check: file
@@ -89,10 +89,10 @@ vep_plugin:
     path: cluster_constant_path!/references/gnomad_pli_per_gene_-_r2.1.1-.txt
   LoFtool:
     exists_check: file
-    path: cluster_constant_path!/references/ensembl-tools-data/cache/Plugins/LoFtool_scores.txt
+    path: cluster_constant_path!/references/ensembl-tools-data-99/cache/Plugins/LoFtool_scores.txt
   MaxEntScan:
     exists_check: directory
     parameters:
       - SWA
       - NCSS
-    path: cluster_constant_path!/references/ensembl-tools-data/cache/Plugins/fordownload
+    path: cluster_constant_path!/references/ensembl-tools-data-99/cache/Plugins/fordownload
diff --git a/templates/mip_rd_dna_panel_config.yaml b/templates/mip_rd_dna_panel_config.yaml
@@ -52,8 +52,8 @@ vep_custom_annotation:
     file_type: vcf
     path: cluster_constant_path!/references/grch37_clinvar_reformated_-20190305-.vcf.gz
     vcf_fields: CLNSIG,CLNVID,CLNREVSTAT
-vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data/cache/
-vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data/cache/Plugins
+vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-99/cache/
+vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-99/cache/Plugins
 vep_plugin:
   dbNSFP:
     exists_check: file
@@ -69,10 +69,10 @@ vep_plugin:
     path: cluster_constant_path!/references/gnomad_pli_per_gene_-_r2.1.1-.txt
   LoFtool:
     exists_check: file
-    path: cluster_constant_path!/references/ensembl-tools-data/cache/Plugins/LoFtool_scores.txt
+    path: cluster_constant_path!/references/ensembl-tools-data-99/cache/Plugins/LoFtool_scores.txt
   MaxEntScan:
     exists_check: directory
     parameters:
       - SWA
       - NCSS
-    path: cluster_constant_path!/references/ensembl-tools-data/cache/Plugins/fordownload
+    path: cluster_constant_path!/references/ensembl-tools-data-99/cache/Plugins/fordownload
diff --git a/templates/mip_rd_dna_vcf_rerun_config.yaml b/templates/mip_rd_dna_vcf_rerun_config.yaml
@@ -64,8 +64,8 @@ vep_custom_annotation:
     file_type: vcf
     path: cluster_constant_path!/references/grch37_clinvar_reformated_-20190305-.vcf.gz
     vcf_fields: CLNSIG,CLNVID,CLNREVSTAT
-vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data/cache/
-vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data/cache/Plugins
+vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-99/cache/
+vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-99/cache/Plugins
 vep_plugin:
   dbNSFP:
     exists_check: file
@@ -81,10 +81,10 @@ vep_plugin:
     path: cluster_constant_path!/references/gnomad_pli_per_gene_-_r2.1.1-.txt
   LoFtool:
     exists_check: file
-    path: cluster_constant_path!/references/ensembl-tools-data/cache/Plugins/LoFtool_scores.txt
+    path: cluster_constant_path!/references/ensembl-tools-data-99/cache/Plugins/LoFtool_scores.txt
   MaxEntScan:
     exists_check: directory
     parameters:
       - SWA
       - NCSS
-    path: cluster_constant_path!/references/ensembl-tools-data/cache/Plugins/fordownload
+    path: cluster_constant_path!/references/ensembl-tools-data-99/cache/Plugins/fordownload
diff --git a/templates/mip_rd_rna_config.yaml b/templates/mip_rd_rna_config.yaml
@@ -27,4 +27,4 @@ arriba_blacklist_path: /arriba_v1.1.0/database/blacklist_hg19_hs37d5_GRCh37_2018
 arriba_cytoband_path: /arriba_v1.1.0/database/cytobands_hg19_hs37d5_GRCh37_2018-02-23.tsv
 arriba_proteindomain_path: /arriba_v1.1.0/database/protein_domains_hg19_hs37d5_GRCh37_2018-03-06.gff3
 picardtools_path: /usr/picard
-vep_directory_cache: cluster_constant_path!/modules/miniconda/envs/MIP_rd_rna/ensembl-tools-97/cache/
+vep_directory_cache: cluster_constant_path!/modules/miniconda/envs/MIP_rd_rna/ensembl-tools-99/cache/