diff --git a/CHANGELOG.md b/CHANGELOG.md index a8ed3aa6a..692bf6fdb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,10 +9,13 @@ This project adheres to [Semantic Versioning](http://semver.org/). - Run UPD and subsequently chromograph on unaffected children - Annotate SV variants with the caller that reported the variant - Produce files for CNV analysis in Gens +- Updated SO terms for new version of VEP +- ExACpLI -> pLI, see [vep issue 108](https://github.com/Ensembl/VEP_plugins/issues/108) ### Tools - Arriba: 2.1.0 -> 2.3.0 +- Chromograph 1.1.4 -> 1.1.5 - DeepVariant: 1.1.0 -> 1.4.0 - ExpansionHunter: 4.0.2 -> 5.0.0 - GATK: 4.2.2.0 -> 4.2.6.1 @@ -24,14 +27,15 @@ This project adheres to [Semantic Versioning](http://semver.org/). - Star Fusion: 1.10.1 -> 1.11.0 - Stranger: 0.8.0 -> 0.8.1 - Stringtie: 2.1.3b -> 2.2.1 -- svdb: 2.4.0 -> 2.6.4 -- Tiddit: 2.12.1 -> 3.1.0 +- Tiddit: 2.12.1 -> 3.3.1 - Trimgalore: 0.6.4 -> 0.6.7 -- VEP: 104.3 -> 106.1 +- VEP: 104.3 -> 107.0 +- svdb: 2.4.0 -> 2.6.4 +- vcf2cytosure v0.5.1 -> v0.8 ### Databases -- clinvar: 211010 -> 220730 +- clinvar: 20211010 -> 20220829 - dbnsfp: 4.1a -> 4.3a (grch38 only) - gnomad: r3.1.1 -> r3.1.2 (grch38 only) - giab: 3.3.2 -> 4.2.1 diff --git a/containers/chromograph/Dockerfile b/containers/chromograph/Dockerfile index b330eacc8..38144e2f9 100644 --- a/containers/chromograph/Dockerfile +++ b/containers/chromograph/Dockerfile @@ -5,9 +5,9 @@ FROM clinicalgenomics/mip_base:2.1 ################## METADATA ###################### LABEL base_image="clinicalgenomics/mip_base:2.1" -LABEL version="12" +LABEL version="13" LABEL software="chromograph" -LABEL software.version="1.1.4" +LABEL software.version="1.1.5" LABEL extra.binaries="chromograph" LABEL maintainer="Clinical-Genomics/MIP" @@ -22,9 +22,9 @@ RUN conda install pip python=3.9 matplotlib && \ WORKDIR /opt/conda/share -RUN wget --no-verbose https://github.com/mikaell/chromograph/archive/refs/tags/v1.1.4.zip && \ - unzip v1.1.4.zip && \ - cd chromograph-1.1.4 && \ +RUN wget --no-verbose https://github.com/mikaell/chromograph/archive/refs/tags/v1.1.5.zip && \ + unzip v1.1.5.zip && \ + cd chromograph-1.1.5 && \ python -m pip install --no-cache-dir . WORKDIR /data/ diff --git a/definitions/install_parameters.yaml b/definitions/install_parameters.yaml index 02a89f318..4512614bb 100644 --- a/definitions/install_parameters.yaml +++ b/definitions/install_parameters.yaml @@ -206,7 +206,7 @@ vep_plugins: data_type: ARRAY default: - dbNSFP - - ExACpLI + - pLI - LoFtool - MaxEntScan - SpliceAI diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml index 2948bd226..026f68625 100755 --- a/definitions/rd_dna_parameters.yaml +++ b/definitions/rd_dna_parameters.yaml @@ -250,6 +250,7 @@ recipe_core_number: sv_varianteffectpredictor: 0 sv_vcfparser: 13 telomerecat_ar: 12 + tiddit: 12 tiddit_coverage: 1 upd_ar: 1 varg_ar: 1 @@ -307,7 +308,7 @@ recipe_memory: sv_annotate: 7 sv_reformat: 24 sv_varianteffectpredictor: 9 - tiddit: 8 + tiddit: 5 upd_ar: 3 variant_annotation: 3 varianteffectpredictor: 7 @@ -380,7 +381,7 @@ recipe_time: sv_varianteffectpredictor: 10 sv_vcfparser: 2 telomerecat_ar: 5 - tiddit: 20 + tiddit: 15 tiddit_coverage: 5 upd_ar: 1 varg_ar: 1 diff --git a/documentation/Setup.md b/documentation/Setup.md index d9ca5f6ad..504ea47c9 100644 --- a/documentation/Setup.md +++ b/documentation/Setup.md @@ -34,8 +34,8 @@ You can speed up, for instance, the Readonly module by also installing the compa - Simple Linux Utility for Resource Management ([SLURM]) (version: 18.08.0) #### **Pipeline: Rare disease** -- [Arriba] (version: 2.1.0) -- [Bcftools] (version: 1.11) +- [Arriba] (version: 2.3.0) +- [Bcftools] (version: 1.15.1) - [BWA] (version: 0.7.17) - [BedTools] (version: 2.30.0) - [Blobfish] (version: 0.0.2 ) @@ -43,13 +43,13 @@ You can speed up, for instance, the Readonly module by also installing the compa - [BWAKit] (version: 0.7.17) - [CADD] (version: 1.6) - [Chanjo] (version: 4.6.0) -- [Chromograph] (version: 1.1.4) +- [Chromograph] (version: 1.1.5) - [Cnvnator] (version: 0.4.1) - [Cyrius] (version: v1.1.1) -- [Expansionhunter] (version 4.0.2) +- [Expansionhunter] (version 5.0.0) - [FastQC] (version: 0.11.9) -- [Deeptrio] (version: 1.2.0) -- [Deepvariant] (version: 1.1.0) +- [Deeptrio] (version: 1.4.0) +- [Deepvariant] (version: 1.4.0) - [Delly] (version 0.8.7) - [GATK] (version: 3.8.1 and 4.2.2.0) - [GENMOD] (version: 3.7.3) @@ -58,10 +58,10 @@ You can speed up, for instance, the Readonly module by also installing the compa - [Htslib] (version: 1.13) - [Manta] (version: 1.6.0) - [Megafusion] (version: 66a3a80) -- [MultiQC] (version: v1.11) +- [MultiQC] (version: v1.12) - [Pdfmerger] (version: 1.0) - [Peddy] (version: 0.4.3) -- [PicardTools] (version: 2.25.0) +- [PicardTools] (version: 2.27.2) - [PLINK] (version: 1.90b3x35) - [Preseq] (version: 3.1.2) - [Rhocall] (version: 0.5.1) @@ -69,9 +69,9 @@ You can speed up, for instance, the Readonly module by also installing the compa - [rtg-tools] (version: 3.12) - [Salmon] (version: 1.4.0) - [Sambamba] (version: 0.6.8) -- [Samtools] (version: 1.11) +- [Samtools] (version: 1.15.1) - [SMNCopyNumberCaller] (version: v1.1.1) -- [STAR-Fusion] (version: 1.10.1) +- [STAR-Fusion] (version: 1.11.0) - [STAR] (version: 2.7.8a) - [Stranger] (version: 0.8.0) - [StringTie] (version: 2.1.3b) @@ -82,7 +82,7 @@ You can speed up, for instance, the Readonly module by also installing the compa - [Varg] (version: 1.2.0) - [Vcf2cytosure] (version: 0.5.1) - [Vcfanno] (version: 0.3.2) -- [VEP] (version: 104.3) with plugin "ExACpLI", "MaxEntScan, LoFtool", "SpliceAI" +- [VEP] (version: 107.0) with plugin "pLI", "MaxEntScan, LoFtool", "SpliceAI" The version number after the software name are tested for compatibility with MIP. diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm index e6e828afe..b3313a39b 100644 --- a/lib/MIP/Constants.pm +++ b/lib/MIP/Constants.pm @@ -90,151 +90,159 @@ Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160; Readonly our %SO_CONSEQUENCE_SEVERITY => ( transcript_ablation => { rank => 1, - genetic_region_annotation => q{exonic} - }, - splice_donor_variant => { - rank => 2, - genetic_region_annotation => q{splicing} + genetic_region_annotation => q{exonic}, }, splice_acceptor_variant => { rank => 2, - genetic_region_annotation => q{splicing} + genetic_region_annotation => q{splicing}, }, - stop_gained => { + splice_donor_variant => { rank => 3, - genetic_region_annotation => q{exonic} + genetic_region_annotation => q{splicing}, }, - frameshift_variant => { + stop_gained => { rank => 4, - genetic_region_annotation => q{exonic} + genetic_region_annotation => q{exonic}, }, - stop_lost => { + frameshift_variant => { rank => 5, - genetic_region_annotation => q{exonic} + genetic_region_annotation => q{exonic}, + }, + stop_lost => { + rank => 6, + genetic_region_annotation => q{exonic}, }, start_lost => { - rank => 5, - genetic_region_annotation => q{exonic} + rank => 7, + genetic_region_annotation => q{exonic}, }, - initiator_codon_variant => { - rank => 6, - genetic_region_annotation => q{exonic} + transcript_amplification => { + rank => 8, + genetic_region_annotation => q{exonic}, }, inframe_insertion => { - rank => 6, - genetic_region_annotation => q{exonic} + rank => 9, + genetic_region_annotation => q{exonic}, }, inframe_deletion => { - rank => 6, - genetic_region_annotation => q{exonic} + rank => 10, + genetic_region_annotation => q{exonic}, }, missense_variant => { - rank => 6, - genetic_region_annotation => q{exonic} + rank => 11, + genetic_region_annotation => q{exonic}, }, protein_altering_variant => { - rank => 6, - genetic_region_annotation => q{exonic} - }, - transcript_amplification => { - rank => 7, - genetic_region_annotation => q{exonic} + rank => 12, + genetic_region_annotation => q{exonic}, }, splice_region_variant => { - rank => 8, - genetic_region_annotation => q{splicing} + rank => 13, + genetic_region_annotation => q{splicing}, + }, + splice_donor_5th_base_variant => { + rank => 14, + genetic_region_annotation => q{splicing}, + }, + splice_donor_region_variant => { + rank => 15, + genetic_region_annotation => q{splicing}, + }, + splice_polypyrimidine_tract_variant => { + rank => 16, + genetic_region_annotation => q{splicing}, }, incomplete_terminal_codon_variant => { - rank => 9, - genetic_region_annotation => q{exonic} + rank => 17, + genetic_region_annotation => q{exonic}, }, - synonymous_variant => { - rank => 10, - genetic_region_annotation => q{exonic} + start_retained_variant => { + rank => 18, + genetic_region_annotation => q{exonic}, }, stop_retained_variant => { - rank => 10, - genetic_region_annotation => q{exonic} + rank => 19, + genetic_region_annotation => q{exonic}, }, - start_retained_variant => { - rank => 10, - genetic_region_annotation => q{exonic} + synonymous_variant => { + rank => 20, + genetic_region_annotation => q{exonic}, }, coding_sequence_variant => { - rank => 11, - genetic_region_annotation => q{exonic} + rank => 21, + genetic_region_annotation => q{exonic}, }, mature_miRNA_variant => { - rank => 12, - genetic_region_annotation => q{ncRNA_exonic} + rank => 22, + genetic_region_annotation => q{ncRNA_exonic}, }, q{5_prime_UTR_variant} => { - rank => 13, - genetic_region_annotation => q{5UTR} + rank => 23, + genetic_region_annotation => q{5UTR}, }, q{3_prime_UTR_variant} => { - rank => 14, - genetic_region_annotation => q{3UTR} + rank => 24, + genetic_region_annotation => q{3UTR}, }, non_coding_transcript_exon_variant => { - rank => 15, - genetic_region_annotation => q{ncRNA_exonic} - }, - non_coding_transcript_variant => { - rank => 15, - genetic_region_annotation => q{ncRNA} + rank => 25, + genetic_region_annotation => q{ncRNA_exonic}, }, intron_variant => { - rank => 16, - genetic_region_annotation => q{intronic} + rank => 26, + genetic_region_annotation => q{intronic}, }, NMD_transcript_variant => { - rank => 17, - genetic_region_annotation => q{ncRNA} + rank => 27, + genetic_region_annotation => q{ncRNA}, + }, + non_coding_transcript_variant => { + rank => 28, + genetic_region_annotation => q{ncRNA}, }, upstream_gene_variant => { - rank => 18, - genetic_region_annotation => q{upstream} + rank => 29, + genetic_region_annotation => q{upstream}, }, downstream_gene_variant => { - rank => 19, - genetic_region_annotation => q{downstream} + rank => 30, + genetic_region_annotation => q{downstream}, }, TFBS_ablation => { - rank => 20, - genetic_region_annotation => q{TFBS} + rank => 31, + genetic_region_annotation => q{TFBS}, }, TFBS_amplification => { - rank => 21, - genetic_region_annotation => q{TFBS} + rank => 32, + genetic_region_annotation => q{TFBS}, }, TF_binding_site_variant => { - rank => 22, - genetic_region_annotation => q{TFBS} - }, - regulatory_region_variant => { - rank => 22, - genetic_region_annotation => q{regulatory_region} + rank => 33, + genetic_region_annotation => q{TFBS}, }, regulatory_region_ablation => { - rank => 23, - genetic_region_annotation => q{regulatory_region} + rank => 34, + genetic_region_annotation => q{regulatory_region}, }, regulatory_region_amplification => { - rank => 24, - genetic_region_annotation => q{regulatory_region} + rank => 35, + genetic_region_annotation => q{regulatory_region}, }, feature_elongation => { - rank => 25, - genetic_region_annotation => q{genomic_feature} + rank => 36, + genetic_region_annotation => q{genomic_feature}, + }, + regulatory_region_variant => { + rank => 37, + genetic_region_annotation => q{regulatory_region}, }, feature_truncation => { - rank => 26, - genetic_region_annotation => q{genomic_feature} + rank => 38, + genetic_region_annotation => q{genomic_feature}, }, intergenic_variant => { - rank => 27, - genetic_region_annotation => q{intergenic} + rank => 39, + genetic_region_annotation => q{intergenic}, }, ); diff --git a/lib/MIP/Program/Tiddit.pm b/lib/MIP/Program/Tiddit.pm index 3c8a9c43c..0dde9cb33 100644 --- a/lib/MIP/Program/Tiddit.pm +++ b/lib/MIP/Program/Tiddit.pm @@ -162,6 +162,7 @@ sub tiddit_sv { ## : $stderrfile_path => Stderrfile path ## : $stderrfile_path_append => Append stderr info to file path ## : $stdoutfile_path => Stdoutfile path +## : $threads => Threads my ($arg_href) = @_; @@ -174,6 +175,7 @@ sub tiddit_sv { my $stderrfile_path; my $stderrfile_path_append; my $stdoutfile_path; + my $threads; my $tmpl = { filehandle => { store => \$filehandle, }, @@ -207,6 +209,11 @@ sub tiddit_sv { store => \$stdoutfile_path, strict_type => 1, }, + threads => { + allow => qr/ \A \d+ \z /xms, + store => \$threads, + strict_type => 1, + }, }; check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!}; @@ -228,6 +235,10 @@ sub tiddit_sv { push @commands, q{--bam} . $SPACE . $infile_path; + if ($threads) { + push @commands, q{--threads} . $SPACE . $threads; + } + push @commands, unix_standard_streams( { diff --git a/lib/MIP/Recipes/Analysis/Expansionhunter.pm b/lib/MIP/Recipes/Analysis/Expansionhunter.pm index 2e9a66908..f788e6aef 100644 --- a/lib/MIP/Recipes/Analysis/Expansionhunter.pm +++ b/lib/MIP/Recipes/Analysis/Expansionhunter.pm @@ -276,9 +276,11 @@ sub analysis_expansionhunter { htslib_bgzip( { - filehandle => $filehandle, - infile_path => $exphun_sample_vcf, - threads => $recipe{core_number}, + filehandle => $filehandle, + infile_path => $exphun_sample_vcf, + stdoutfile_path => $exphun_sample_vcf . q{.gz}, + threads => $recipe{core_number}, + write_to_stdout => 1, } ); say {$filehandle} $NEWLINE; @@ -385,8 +387,7 @@ sub analysis_expansionhunter { { format => q{vcf}, id => $sample_id, - path => $exphun_sample_file{$sample_id}{out_vcf} . q{.gz}, - path_index => $exphun_sample_file{$sample_id}{out_vcf} . q{.gz.tbi}, + path => $exphun_sample_file{$sample_id}{out_vcf}, recipe_name => $recipe_name, sample_info_href => $sample_info_href, tag => q{str_variants}, diff --git a/lib/MIP/Recipes/Analysis/Glnexus.pm b/lib/MIP/Recipes/Analysis/Glnexus.pm index 7d16a064a..9825de9eb 100644 --- a/lib/MIP/Recipes/Analysis/Glnexus.pm +++ b/lib/MIP/Recipes/Analysis/Glnexus.pm @@ -317,6 +317,9 @@ sub _build_sed_script { ## Prepend header to line . q{s//} . $header_info . q{\n&/; } + ## Skip the #CHROM line + . q{/^#CHROM\t/n; } + ## Append new info tag to all INFO columns (8th) . q{s/[^\t]*/&;} . $info_tag . q{/8} . $SINGLE_QUOTE; diff --git a/lib/MIP/Recipes/Analysis/Tiddit.pm b/lib/MIP/Recipes/Analysis/Tiddit.pm index 6e5a5201b..ec9c1420d 100644 --- a/lib/MIP/Recipes/Analysis/Tiddit.pm +++ b/lib/MIP/Recipes/Analysis/Tiddit.pm @@ -136,11 +136,6 @@ sub analysis_tiddit { ## Retrieve logger object my $log = Log::Log4perl->get_logger($LOG_NAME); - ## Unpack parameters - my $max_cores_per_node = $active_parameter_href->{max_cores_per_node}; - my $modifier_core_number = - scalar( @{ $active_parameter_href->{sample_ids} } ); - my %recipe = parse_recipe_prerequisites( { active_parameter_href => $active_parameter_href, @@ -170,31 +165,15 @@ sub analysis_tiddit { # Create anonymous filehandle my $filehandle = IO::Handle->new(); - ## Update number of cores and memory depending on how many samples that are processed - my $core_number = get_core_number( - { - max_cores_per_node => $max_cores_per_node, - modifier_core_number => $modifier_core_number, - recipe_core_number => $recipe{core_number}, - } - ); - my $memory_allocation = update_memory_allocation( - { - node_ram_memory => $active_parameter_href->{node_ram_memory}, - parallel_processes => $core_number, - process_memory_allocation => $recipe{memory}, - } - ); - ## Creates recipe directories (info & data & script), recipe script filenames and writes sbatch header my ( $recipe_file_path, $recipe_info_path ) = setup_script( { active_parameter_href => $active_parameter_href, - core_number => $core_number, + core_number => $recipe{core_number}, directory_id => $case_id, filehandle => $filehandle, job_id_href => $job_id_href, - memory_allocation => $memory_allocation, + memory_allocation => $recipe{memory}, process_time => $recipe{time}, recipe_directory => $recipe_name, recipe_name => $recipe_name, @@ -208,7 +187,7 @@ sub analysis_tiddit { ## Collect infiles for all sample_ids to enable migration to temporary directory SAMPLE_ID: - while ( my ( $sample_id_index, $sample_id ) = each @{ $active_parameter_href->{sample_ids} } ) { + foreach my $sample_id ( @{ $active_parameter_href->{sample_ids} } ) { ## Get the io infiles per chain and id my %sample_io = get_io_files( @@ -229,23 +208,10 @@ sub analysis_tiddit { } say {$filehandle} q{wait}, $NEWLINE; - # Start counter - my $process_batches_count = 1; - ## Tiddit sv calling per sample id SAMPLE_ID: - while ( my ( $sample_id_index, $sample_id ) = each @{ $active_parameter_href->{sample_ids} } ) { + foreach my $sample_id ( @{ $active_parameter_href->{sample_ids} } ) { - $process_batches_count = print_wait( - { - filehandle => $filehandle, - max_process_number => $core_number, - process_batches_count => $process_batches_count, - process_counter => $sample_id_index, - } - ); - - ## Tiddit tiddit_sv( { filehandle => $filehandle, @@ -254,11 +220,11 @@ sub analysis_tiddit { $active_parameter_href->{tiddit_minimum_number_supporting_pairs}, outfile_path_prefix => $tiddit_sample_file_info{$sample_id}{out}, referencefile_path => $active_parameter_href->{human_genome_reference}, + threads => $recipe{core_number} } ); - say {$filehandle} $AMPERSAND . $SPACE . $NEWLINE; + say {$filehandle} $NEWLINE; } - say {$filehandle} q{wait}, $NEWLINE; ## Get parameters ## Tiddit sample outfiles needs to be lexiographically sorted for svdb merge diff --git a/lib/MIP/Recipes/Install/Vep.pm b/lib/MIP/Recipes/Install/Vep.pm index 9b1b96ffb..b7bf22165 100644 --- a/lib/MIP/Recipes/Install/Vep.pm +++ b/lib/MIP/Recipes/Install/Vep.pm @@ -178,7 +178,7 @@ q{By default VEP cache and plugins will be downloaded to /ensembl my %finish_plugin_installation = ( MaxEntScan => \&_install_maxentscan_plugin, LoFtool => \&_install_loftool_plugin, - ExACpLI => \&_install_exacpli_plugin, + pLI => \&_install_pli_plugin, ); PLUGIN: @@ -285,16 +285,16 @@ sub _install_loftool_plugin { { outfile_path => catfile( $plugin_dir_path, q{LoFtool_scores.txt} ), url => -q{https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/106/LoFtool_scores.txt}, +q{https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/107/LoFtool_scores.txt}, } ); return @cmds; } -sub _install_exacpli_plugin { +sub _install_pli_plugin { -## Function : Write command that downloads file required by ExACpLI +## Function : Write command that downloads file required by pLI ## Returns : @cmds ## Arguments: $plugin_dir_path => Plugin path @@ -316,9 +316,9 @@ sub _install_exacpli_plugin { my @cmds = wget( { - outfile_path => catfile( $plugin_dir_path, q{ExACpLI_values.txt} ), + outfile_path => catfile( $plugin_dir_path, q{pLI_values.txt} ), url => -q{https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/106/ExACpLI_values.txt}, + q{https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/107/pLI_values.txt}, } ); diff --git a/t/analysis_vep_sv_wes.t b/t/analysis_vep_sv_wes.t index ef3c5395e..527fc0ea5 100644 --- a/t/analysis_vep_sv_wes.t +++ b/t/analysis_vep_sv_wes.t @@ -37,7 +37,7 @@ BEGIN { ## Modules with import my %perl_module = ( q{MIP::Recipes::Analysis::Vep} => [qw{ analysis_vep_sv_wes }], - q{MIP::Test::Fixtures} => [qw{ test_add_io_for_recipe test_log test_mip_hashes }], + q{MIP::Test::Fixtures} => [qw{ test_add_io_for_recipe test_log test_mip_hashes }], ); test_import( { perl_module_href => \%perl_module, } ); @@ -77,8 +77,8 @@ $active_parameter{vep_custom_annotation}{a_ref} = { annotation_type => q{exact}, }; $active_parameter{vep_directory_cache} = q{a_cache}; -$active_parameter{sv_vep_plugin}{ExACpLI} = { path => q{a_path}, }; -$active_parameter{sv_vep_features} = [qw{ refseq }]; +$active_parameter{sv_vep_plugin}{pLI} = { path => q{a_path}, }; +$active_parameter{sv_vep_features} = [qw{ refseq }]; my %file_info = test_mip_hashes( { mip_hash_name => q{file_info}, @@ -100,11 +100,11 @@ my %parameter = test_mip_hashes( test_add_io_for_recipe( { - file_info_href => \%file_info, - id => $case_id, - parameter_href => \%parameter, - recipe_name => $recipe_name, - step => q{vcf}, + file_info_href => \%file_info, + id => $case_id, + parameter_href => \%parameter, + recipe_name => $recipe_name, + step => q{vcf}, } ); diff --git a/t/analysis_vep_sv_wgs.t b/t/analysis_vep_sv_wgs.t index ee72a894a..e6c7ca45e 100644 --- a/t/analysis_vep_sv_wgs.t +++ b/t/analysis_vep_sv_wgs.t @@ -37,7 +37,7 @@ BEGIN { ## Modules with import my %perl_module = ( q{MIP::Recipes::Analysis::Vep} => [qw{ analysis_vep_sv_wgs }], - q{MIP::Test::Fixtures} => [qw{ test_add_io_for_recipe test_log test_mip_hashes }], + q{MIP::Test::Fixtures} => [qw{ test_add_io_for_recipe test_log test_mip_hashes }], ); test_import( { perl_module_href => \%perl_module, } ); @@ -77,8 +77,8 @@ $active_parameter{vep_custom_annotation}{a_ref} = { annotation_type => q{exact}, }; $active_parameter{vep_directory_cache} = q{a_cache}; -$active_parameter{sv_vep_plugin}{ExACpLI} = { path => q{a_path}, }; -$active_parameter{sv_vep_features} = [qw{ refseq }]; +$active_parameter{sv_vep_plugin}{pLI} = { path => q{a_path}, }; +$active_parameter{sv_vep_features} = [qw{ refseq }]; my %file_info = test_mip_hashes( { @@ -102,11 +102,11 @@ my %parameter = test_mip_hashes( test_add_io_for_recipe( { - file_info_href => \%file_info, - id => $case_id, - parameter_href => \%parameter, - recipe_name => $recipe_name, - step => q{vcf}, + file_info_href => \%file_info, + id => $case_id, + parameter_href => \%parameter, + recipe_name => $recipe_name, + step => q{vcf}, } ); diff --git a/t/check_vep_plugin.t b/t/check_vep_plugin.t index 221db7c3c..572f89d51 100644 --- a/t/check_vep_plugin.t +++ b/t/check_vep_plugin.t @@ -116,7 +116,7 @@ like( $trap->die, qr/Is\s+not\s+a/xms, q{Not a hash ref} ); delete $vep_plugin{not_valid_annotation}; ## Given a plugin that is missing -$vep_plugin{MockPlugin} = $rd_dna_config{vep_plugin}{ExACpLI}; +$vep_plugin{MockPlugin} = $rd_dna_config{vep_plugin}{pLI}; trap { check_vep_plugin( { diff --git a/t/data/references/ensembl-tools-data-104/cache/Plugins/ExACpLI.pm b/t/data/references/ensembl-tools-data-104/cache/Plugins/pLI.pm similarity index 100% rename from t/data/references/ensembl-tools-data-104/cache/Plugins/ExACpLI.pm rename to t/data/references/ensembl-tools-data-104/cache/Plugins/pLI.pm diff --git a/t/data/references/grch37_clinvar_reformated_-20211010-.vcf.gz b/t/data/references/grch37_clinvar_reformated_-20220829-.vcf.gz similarity index 100% rename from t/data/references/grch37_clinvar_reformated_-20211010-.vcf.gz rename to t/data/references/grch37_clinvar_reformated_-20220829-.vcf.gz diff --git a/t/data/references/grch37_clinvar_reformated_-20211010-.vcf.gz.tbi b/t/data/references/grch37_clinvar_reformated_-20220829-.vcf.gz.tbi similarity index 100% rename from t/data/references/grch37_clinvar_reformated_-20211010-.vcf.gz.tbi rename to t/data/references/grch37_clinvar_reformated_-20220829-.vcf.gz.tbi diff --git a/t/data/test_data/install_active_parameters.yaml b/t/data/test_data/install_active_parameters.yaml index edcf51528..bf7cc19fc 100644 --- a/t/data/test_data/install_active_parameters.yaml +++ b/t/data/test_data/install_active_parameters.yaml @@ -377,7 +377,7 @@ vep_assemblies: vep_auto_flag: cfp vep_plugins: - dbNSFP - - ExACpLI + - pLI - LoFtool - MaxEntScan - SpliceAI diff --git a/t/data/test_data/miptest_install_config.yaml b/t/data/test_data/miptest_install_config.yaml index 457c59f02..8a2252a35 100644 --- a/t/data/test_data/miptest_install_config.yaml +++ b/t/data/test_data/miptest_install_config.yaml @@ -253,7 +253,7 @@ container: uri: docker.io/jemten/vcf2cytosure:0.5.1 vep_plugins: - dbNSFP - - ExACpLI + - pLI - LoFtool - MaxEntScan - SpliceAI diff --git a/t/data/test_data/test.vcf b/t/data/test_data/test.vcf index 53390ed9a..2baa981d9 100644 --- a/t/data/test_data/test.vcf +++ b/t/data/test_data/test.vcf @@ -10,7 +10,7 @@ ##ALT= ##source=HaplotypeCaller ##bcftools_normVersion=1.9+htslib-1.9 -##INFO= +##INFO= ##Software=C||||||,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|transcript|ENST00000515242|transcribed_unprocessed_pseudogene|2/3|n.463G>C||||||,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|transcript|ENST00000518655|transcribed_unprocessed_pseudogene|2/4|n.479G>C||||||,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000438504|unprocessed_pseudogene||n.*1644C>G|||||1644|,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000541675|unprocessed_pseudogene||n.*1644C>G|||||1644|,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000423562|unprocessed_pseudogene||n.*1644C>G|||||1644|,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147|unprocessed_pseudogene||n.*1685C>G|||||1685|,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000538476|unprocessed_pseudogene||n.*1692C>G|||||1692|,C|intron_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305|transcribed_unprocessed_pseudogene|3/5|n.182+22G>C||||||;Annotation=DDX11L1,WASH7P;BaseQRankSum=0;CADD=3.695;CSQ=C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||1644|-1||HGNC|38034||||||||||Ensembl|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||1644|-1||HGNC|38034|YES|||||||||Ensembl|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|intron_variant&non_coding_transcript_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene||3/5|ENST00000450305.2:n.182+22G>C|||||||||1||HGNC|37102||||||||||Ensembl|G|G||||||||||||7.609|1.139|11.897|7.154|1.939|-9.983|-0.263|-8.045|9.219|-1.563|7.656|7.656||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|2/3||ENST00000456328.2:n.466G>C||466|||||||1||HGNC|37102|YES|||||||||Ensembl|G|G||||||||||||3.895|7.656|11.897|9.092|1.939|-9.983|-0.263|-8.045|9.219|-1.563|7.656|7.656|9.219|-1.563|7.656|0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||1685|-1||HGNC|38034||||||||||Ensembl|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|2/3||ENST00000515242.2:n.463G>C||463|||||||1||HGNC|37102||||||||||Ensembl|G|G||||||||||||-0.591|7.656|11.897|9.092|1.939|-9.983|-0.263|-8.045|9.219|-1.563|7.656|7.656|9.219|-1.563|7.656|0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|2/4||ENST00000518655.2:n.479G>C||479|||||||1||HGNC|37102||||||||||Ensembl|G|G||||||||||||11.709|7.656|4.227|9.092|1.939|-9.983|-0.263|-8.045|9.219|-1.563|7.656|7.656|9.219|-1.563|7.656|0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||1692|-1||HGNC|38034||||||||||Ensembl|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||1644|-1||HGNC|38034||||||||||Ensembl|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|WASH7P|653635|Transcript|NR_024540.1|pseudogene|||||||||||1643|-1||EntrezGene|38034|YES|||||||||RefSeq|G|G|OK|||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|DDX11L1|100287102|Transcript|NR_046018.2|pseudogene|2/3||NR_046018.2:n.461G>C||461|||||||1||EntrezGene|37102|YES|||||||||RefSeq|G|G||||||||||||3.895|7.656|11.897|9.092|1.939|-9.983|-0.263|-8.045|9.219|-1.563|7.656|7.656|9.219|-1.563|7.656|0.982898&0.981582&0.992904&0.987856&0.986907&0.994232,C|downstream_gene_variant|MODIFIER|MIR6859-1|102466751|Transcript|NR_106918.1|miRNA|||||||||||4650|-1||EntrezGene||YES|||||||||RefSeq|G|G||||||||||||||||0.904|0.625|1.528|1.528|-7.625|-3.049|-9.575|-10.674||||0.982898&0.981582&0.992904&0.987856&0.986907&0.994232;DP=138;ExcessHet=4.7712;FS=0;GNOMADAF=0.0494;GNOMADAF_popmax=0.1274;MLEAC=2;MLEAF=0.333;MQ=25.62;MQRankSum=-0.086;NEGATIVE_TRAIN_SITE;Obs=230;QD=3.7;RankResult=-12|0|0|-12|5|0|3|0|0|3;RankScore=livingox:-13;ReadPosRankSum=0.819;SOR=0.09;SWEGENAC_Hemi=0;SWEGENAC_Het=154;SWEGENAC_Hom=0;SWEGENAF=0.077;VQSLOD=-3.219;culprit=QD;most_severe_consequence=38034:C|downstream_gene_variant,37102:C|splice_region_variant GT:AD:DP:GQ:PL 0/1:33,7:40:89:89,0,891 0/1:28,11:39:99:214,0,726 0/0:59,0:59:53:0,53,2332 diff --git a/t/parse_vep_csq_schema.t b/t/parse_vep_csq_schema.t index deb0008eb..a886a21d5 100644 --- a/t/parse_vep_csq_schema.t +++ b/t/parse_vep_csq_schema.t @@ -22,16 +22,13 @@ use Readonly; use lib catdir( dirname($Bin), q{lib} ); use MIP::Constants qw{ $COMMA $SPACE }; - BEGIN { use MIP::Test::Fixtures qw{ test_import }; ### Check all internal dependency modules and imports ## Modules with import - my %perl_module = ( - q{MIP::Vcfparser} => [qw{ parse_vep_csq_schema }], -); + my %perl_module = ( q{MIP::Vcfparser} => [qw{ parse_vep_csq_schema }], ); test_import( { perl_module_href => \%perl_module, } ); } @@ -51,7 +48,7 @@ Readonly my $HGNC_ID_CSQ_FIELD_INDEX => 22; ## Given a VEP CSQ line in meta data when parse_vep is true my $vep_csq_schema_header = -q{##INFO=}; +q{##INFO=}; my %meta_data = ( INFO => { CSQ => $vep_csq_schema_header, }, ); my $most_severe_consequence_header = q{##INFO=}; @@ -69,8 +66,7 @@ my $is_ok = parse_vep_csq_schema( ok( $is_ok, q{Parsed VEP CSQ header line} ); ## Then HGNC ID key and corresponding index should have been added to hash -is( $vep_format_field_column{HGNC_ID}, - $HGNC_ID_CSQ_FIELD_INDEX, q{Set HGNC ID field in hash} ); +is( $vep_format_field_column{HGNC_ID}, $HGNC_ID_CSQ_FIELD_INDEX, q{Set HGNC ID field in hash} ); ## Then "most severe consequence" VCF header line should been added to meta data is( diff --git a/t/tiddit_sv.t b/t/tiddit_sv.t index d32484ade..d826d4a1b 100644 --- a/t/tiddit_sv.t +++ b/t/tiddit_sv.t @@ -36,6 +36,7 @@ BEGIN { ## Constants Readonly my $N_SUPPORTING_PAIRS => 50; +Readonly my $THREADS => 8; use MIP::Program::Tiddit qw{ tiddit_sv }; @@ -99,6 +100,10 @@ my %specific_argument = ( input => catfile(qw{ a test reference_path }), expected_output => q{--ref} . $SPACE . catfile(qw{ a test reference_path }), }, + threads => { + input => $THREADS, + expected_output => q{--threads} . $SPACE . $THREADS, + }, ); ## Coderef - enables generalized use of generate call diff --git a/t/update_with_dynamic_config_parameters.t b/t/update_with_dynamic_config_parameters.t index 5c6d7b89c..0446a42dc 100644 --- a/t/update_with_dynamic_config_parameters.t +++ b/t/update_with_dynamic_config_parameters.t @@ -55,7 +55,7 @@ my %active_parameter = ( { another_hash => [ catfile(q{cluster_constant_path!}), ] }, ], sv_vep_plugin => { - ExACpLI => { + pLI => { exists_check => q{file}, path => catfile(qw{ cluster_constant_path! analysis_constant_path! pli.txt }), }, @@ -90,7 +90,7 @@ is( $active_parameter{sample_info_file}, $updated_sample_info_file, q{Updated sample_info_file path} ); my $updated_sv_vep_pli = catfile(qw{ root dir_1 dir_2 case_1 analysis pli.txt }); -is( $active_parameter{sv_vep_plugin}{ExACpLI}{path}, +is( $active_parameter{sv_vep_plugin}{pLI}{path}, $updated_sv_vep_pli, q{Updated sv_vep_plugin pli path} ); my $updated_sv_vep_loftool = catfile(qw{ root dir_1 dir_2 case_1 analysis loftool.txt }); diff --git a/t/write_meta_data.t b/t/write_meta_data.t index 5b158bb8f..aba3d288e 100644 --- a/t/write_meta_data.t +++ b/t/write_meta_data.t @@ -22,7 +22,6 @@ use Readonly; use lib catdir( dirname($Bin), q{lib} ); use MIP::Constants qw{ $COLON $COMMA $NEWLINE $SPACE }; - BEGIN { use MIP::Test::Fixtures qw{ test_import }; @@ -32,7 +31,7 @@ BEGIN { my %perl_module = ( q{MIP::File::Format::Vcf} => [qw{ parse_vcf_header }], q{MIP::Vcfparser} => [qw{ write_meta_data }], -); + ); test_import( { perl_module_href => \%perl_module, } ); } @@ -119,7 +118,7 @@ my $expected_header = <<'EOF'; ##FORMAT= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##contig= ##contig= @@ -137,7 +136,7 @@ my $expected_select_header = <<'EOF'; ##FORMAT= ##INFO= ##INFO= -##INFO= +##INFO= ##INFO= ##contig= ##contig= @@ -149,7 +148,6 @@ EOF ## Then header should be written to vcf out file is( $file_content, $expected_header, q{Wrote meta-data for vcf outfile} ); -is( $select_file_content, $expected_select_header, - q{Wrote meta-data for select vcf outfile} ); +is( $select_file_content, $expected_select_header, q{Wrote meta-data for select vcf outfile} ); done_testing(); diff --git a/templates/grch38_mip_rd_dna_config.yaml b/templates/grch38_mip_rd_dna_config.yaml index 9cd781074..3e3f26509 100755 --- a/templates/grch38_mip_rd_dna_config.yaml +++ b/templates/grch38_mip_rd_dna_config.yaml @@ -77,7 +77,7 @@ qccollect_sampleinfo_file: cluster_constant_path!/case_id!/analysis_constant_pat picardtools_path: /usr/picard/ sv_genmod_models_case_type: cmms sv_vep_plugin: - ExACpLI: + pLI: exist_check: - type: file path: cluster_constant_path!/references/gnomad_pli_per_gene_-_r2.1.1-.txt @@ -111,7 +111,7 @@ vep_plugin: - phyloP100way_vertebrate - phastCons100way_vertebrate - REVEL_rankscore - ExACpLI: + pLI: exist_check: - type: file path: cluster_constant_path!/references/gnomad_pli_per_gene_-_r2.1.1-.txt diff --git a/templates/mip_download_rd_dna_config_-1.0-.yaml b/templates/mip_download_rd_dna_config_-1.0-.yaml index 21396b18f..721a41447 100644 --- a/templates/mip_download_rd_dna_config_-1.0-.yaml +++ b/templates/mip_download_rd_dna_config_-1.0-.yaml @@ -27,7 +27,7 @@ reference: - v1.0 clinvar: - 20211010 - - 20220730 + - 20220829 dbnsfp: - 3.5a - 4.1a @@ -332,13 +332,13 @@ reference_feature: outfile_index: grch37_clinvar_-20211010-.vcf.gz.tbi outfile_check_method: md5sum url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/ - 20220730: - file: clinvar_20220730.vcf.gz - file_check: clinvar_20220730.vcf.gz.md5 - file_index: clinvar_20220730.vcf.gz.tbi - outfile: grch37_clinvar_-20220730-.vcf.gz - outfile_check: grch37_clinvar_-20220730-.vcf.gz.md5 - outfile_index: grch37_clinvar_-20220730-.vcf.gz.tbi + 20220829: + file: clinvar_20220829.vcf.gz + file_check: clinvar_20220829.vcf.gz.md5 + file_index: clinvar_20220829.vcf.gz.tbi + outfile: grch37_clinvar_-20220829-.vcf.gz + outfile_check: grch37_clinvar_-20220829-.vcf.gz.md5 + outfile_index: grch37_clinvar_-20220829-.vcf.gz.tbi outfile_check_method: md5sum url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/ grch38: @@ -351,13 +351,13 @@ reference_feature: outfile_index: grch38_clinvar_-20211010-.vcf.gz.tbi outfile_check_method: md5sum url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/ - 20220730: - file: clinvar_20220730.vcf.gz - file_check: clinvar_20220730.vcf.gz.md5 - file_index: clinvar_20220730.vcf.gz.tbi - outfile: grch38_clinvar_-20220730-.vcf.gz - outfile_check: grch38_clinvar_-20220730-.vcf.gz.md5 - outfile_index: grch38_clinvar_-20220730-.vcf.gz.tbi + 20220829: + file: clinvar_20220829.vcf.gz + file_check: clinvar_20220829.vcf.gz.md5 + file_index: clinvar_20220829.vcf.gz.tbi + outfile: grch38_clinvar_-20220829-.vcf.gz + outfile_check: grch38_clinvar_-20220829-.vcf.gz.md5 + outfile_index: grch38_clinvar_-20220829-.vcf.gz.tbi outfile_check_method: md5sum url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/ dbnsfp: @@ -701,7 +701,7 @@ reference_feature: file_index: HG005_GRCh37_1_22_v4.2.1_benchmark.vcf.gz.tbi outfile: grch37_nist_hg005_-na24631_v4.2.1-.vcf.gz outfile_index: grch37_nist_hg005_-na24631_v4.2.1-.vcf.gz.tbi - url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh37/ + url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv4.2.1/GRCh37/ grch38: na12878_v3.3.2_bed: file: HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed diff --git a/templates/mip_dragen_rd_dna_config.yaml b/templates/mip_dragen_rd_dna_config.yaml index 26f0a81b4..52f80fdc5 100644 --- a/templates/mip_dragen_rd_dna_config.yaml +++ b/templates/mip_dragen_rd_dna_config.yaml @@ -50,7 +50,7 @@ fqf_annotations: picardtools_path: /usr/picard sv_genmod_models_case_type: cmms sv_vep_plugin: - ExACpLI: + pLI: exist_check: - type: file path: cluster_constant_path!/references/gnomad_pli_per_gene_-_r2.1.1-.txt @@ -68,7 +68,7 @@ vep_custom_annotation: force_report_coordinates: 0 key: CLINVAR file_type: vcf - path: cluster_constant_path!/references/grch37_clinvar_reformated_-20211010-.vcf.gz + path: cluster_constant_path!/references/grch37_clinvar_reformated_-20220829-.vcf.gz vcf_fields: CLNSIG,CLNVID,CLNREVSTAT vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-104/cache/ vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins @@ -84,7 +84,7 @@ vep_plugin: - phyloP100way_vertebrate - phastCons100way_vertebrate - REVEL_rankscore - ExACpLI: + pLI: exist_check: - type: file path: cluster_constant_path!/references/gnomad_pli_per_gene_-_r2.1.1-.txt diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml index 26227bbeb..6f7afb9c6 100644 --- a/templates/mip_install_config.yaml +++ b/templates/mip_install_config.yaml @@ -48,7 +48,7 @@ container: chromograph: executable: chromograph: - uri: docker.io/clinicalgenomics/chromograph:1.1.4 + uri: docker.io/clinicalgenomics/chromograph:1.1.5 cyrius: executable: star_caller.py: @@ -221,7 +221,7 @@ container: tiddit: executable: tiddit: - uri: quay.io/biocontainers/tiddit:3.1.0--py39h5094d80_1 + uri: quay.io/biocontainers/tiddit:3.3.1--py39h5094d80_0 trim-galore: executable: trim_galore: @@ -252,8 +252,8 @@ container: vep: executable: vep: - uri: docker.io/ensemblorg/ensembl-vep:release_106.1 + uri: docker.io/ensemblorg/ensembl-vep:release_107.0 vcf2cytosure: executable: vcf2cytosure: - uri: docker.io/jemten/vcf2cytosure:0.5.1 + uri: docker.io/clinicalgenomics/vcf2cytosure:v0.8 diff --git a/templates/mip_rd_dna_config.yaml b/templates/mip_rd_dna_config.yaml index b21b75ba4..017804c1f 100755 --- a/templates/mip_rd_dna_config.yaml +++ b/templates/mip_rd_dna_config.yaml @@ -57,7 +57,7 @@ picardtools_path: /usr/picard qccollect_sampleinfo_file: cluster_constant_path!/case_id!/analysis_constant_path!/case_id!_qc_sample_info.yaml sv_genmod_models_case_type: cmms sv_vep_plugin: - ExACpLI: + pLI: exist_check: - type: file path: cluster_constant_path!/references/gnomad_pli_per_gene_-_r2.1.1-.txt @@ -75,7 +75,7 @@ vep_custom_annotation: force_report_coordinates: 0 key: CLINVAR file_type: vcf - path: cluster_constant_path!/references/grch37_clinvar_reformated_-20211010-.vcf.gz + path: cluster_constant_path!/references/grch37_clinvar_reformated_-20220829-.vcf.gz vcf_fields: CLNSIG,CLNVID,CLNREVSTAT vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-104/cache/ vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins @@ -92,7 +92,7 @@ vep_plugin: - phastCons100way_vertebrate - REVEL_rankscore - rs_dbSNP150 - ExACpLI: + pLI: exist_check: - type: file path: cluster_constant_path!/references/gnomad_pli_per_gene_-_r2.1.1-.txt diff --git a/templates/mip_rd_dna_panel_config.yaml b/templates/mip_rd_dna_panel_config.yaml index 84dde3c6d..a939c4df7 100755 --- a/templates/mip_rd_dna_panel_config.yaml +++ b/templates/mip_rd_dna_panel_config.yaml @@ -49,7 +49,7 @@ vep_custom_annotation: force_report_coordinates: 0 key: CLINVAR file_type: vcf - path: cluster_constant_path!/references/grch37_clinvar_reformated_-20211010-.vcf.gz + path: cluster_constant_path!/references/grch37_clinvar_reformated_-20220829-.vcf.gz vcf_fields: CLNSIG,CLNVID,CLNREVSTAT vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-104/cache/ vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins @@ -65,7 +65,7 @@ vep_plugin: - phyloP100way_vertebrate - phastCons100way_vertebrate - REVEL_rankscore - ExACpLI: + pLI: exist_check: - type: file path: cluster_constant_path!/references/gnomad_pli_per_gene_-_r2.1.1-.txt diff --git a/templates/mip_rd_dna_vcf_rerun_config.yaml b/templates/mip_rd_dna_vcf_rerun_config.yaml index 0a459b86e..2b3cf46f5 100644 --- a/templates/mip_rd_dna_vcf_rerun_config.yaml +++ b/templates/mip_rd_dna_vcf_rerun_config.yaml @@ -52,7 +52,7 @@ sv_fqa_vcfanno_filters: picardtools_path: /usr/picard sv_genmod_models_case_type: cmms sv_vep_plugin: - ExACpLI: + pLI: exist_check: - type: file path: cluster_constant_path!/references/gnomad_pli_per_gene_-_r2.1.1-.txt @@ -70,7 +70,7 @@ vep_custom_annotation: force_report_coordinates: 0 key: CLINVAR file_type: vcf - path: cluster_constant_path!/references/grch37_clinvar_reformated_-20211010-.vcf.gz + path: cluster_constant_path!/references/grch37_clinvar_reformated_-20220829-.vcf.gz vcf_fields: CLNSIG,CLNVID,CLNREVSTAT vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-104/cache/ vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-104/cache/Plugins @@ -86,7 +86,7 @@ vep_plugin: - phyloP100way_vertebrate - phastCons100way_vertebrate - REVEL_rankscore - ExACpLI: + pLI: exist_check: - type: file path: cluster_constant_path!/references/gnomad_pli_per_gene_-_r2.1.1-.txt