Merge remote-tracking branch 'upstream/dev' into refactor-inputs

genomic-medicine-sweden · Oct 30, 2024 · 42bc326 · 42bc326
2 parents bd1eb18 + d444307
commit 42bc326
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -30,6 +30,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#431](https://github.com/genomic-medicine-sweden/nallo/pull/431) - Added files needed to automatically build and publish docs to GitHub Pages
 - [#435](https://github.com/genomic-medicine-sweden/nallo/pull/435) - Added nf-test to rank variants
 - [#445](https://github.com/genomic-medicine-sweden/nallo/pull/445) - Added FOUND_IN tag and nf-test to rank variants
+- [#446](https://github.com/genomic-medicine-sweden/nallo/pull/446) - Added the vcfstatsreport from DeepVariant to snv calling
+- [#450](https://github.com/genomic-medicine-sweden/nallo/pull/450) - Added ranking of SVs (and CNVs)
 
 ### `Changed`
 

diff --git a/README.md b/README.md
@@ -48,7 +48,7 @@
 
 ##### Ranking
 
-- Rank SNVs with [GENMOD](https://github.com/Clinical-Genomics/genmod)
+- Rank SNVs, INDELs and SVs with [GENMOD](https://github.com/Clinical-Genomics/genmod)
 
 ## Usage
 

diff --git a/conf/modules/annotate_consequence_pli.config b/conf/modules/annotate_consequence_pli.config
@@ -12,6 +12,10 @@
 */
 
 process {
+
+    //
+    // SNVs
+    //
     withName: '.*:ANN_CSQ_PLI_SNV:.*' {
         publishDir = [
             enabled: false
@@ -29,4 +33,25 @@ process {
     withName: '.*ANN_CSQ_PLI_SNV:TABIX_BGZIPTABIX' {
         ext.prefix = { "${meta.id}_snv_csq_pli" }
     }
+
+    //
+    // SVs
+    //
+    withName: '.*:ANN_CSQ_PLI_SVS:.*' {
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: '.*ANN_CSQ_PLI_SVS:ADD_MOST_SEVERE_CSQ' {
+        ext.prefix = { "${meta.id}_svs_csq" }
+    }
+
+    withName: '.*ANN_CSQ_PLI_SVS:ADD_MOST_SEVERE_PLI' {
+        ext.prefix = { "${meta.id}_svs_csq_pli" }
+    }
+
+    withName: '.*ANN_CSQ_PLI_SVS:TABIX_BGZIPTABIX' {
+        ext.prefix = { "${meta.id}_svs_csq_pli" }
+    }
 }
diff --git a/conf/modules/annotate_svs.config b/conf/modules/annotate_svs.config
@@ -42,15 +42,15 @@ process {
         publishDir = [
             path: { "${params.outdir}/svs/family/${meta.id}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') || !params.skip_rank_variants ? null : filename }
         ]
     }
 
     withName: '.*ANNOTATE_SVS:TABIX_ENSEMBLVEP_SV' {
         publishDir = [
             path: { "${params.outdir}/svs/family/${meta.id}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') || !params.skip_rank_variants ? null : filename }
         ]
     }
 

diff --git a/conf/modules/rank_variants.config b/conf/modules/rank_variants.config
@@ -11,18 +11,16 @@
 ----------------------------------------------------------------------------------------
 */
 
-//
-// Score and rank SNVs
-//
-
 process {
 
+    //
+    // Score and rank SNVs
+    //
     withName: '.*:RANK_VARIANTS_SNV:.*' {
         publishDir = [
             enabled: false,
         ]
     }
-
     withName: '.*:RANK_VARIANTS_SNV:GENMOD_ANNOTATE' {
         ext.prefix = { "${meta.id}_snv_genmod_annotate" }
         ext.args = { [
@@ -31,20 +29,53 @@ process {
             '--temp_dir ./'
             ].join(' ') }
     }
-
     withName: '.*:RANK_VARIANTS_SNV:GENMOD_MODELS' {
         ext.prefix = { "${meta.id}_snv_genmod_models" }
         ext.args = "--whole_gene --temp_dir ./"
     }
-
     withName: '.*:RANK_VARIANTS_SNV:GENMOD_SCORE' {
         ext.prefix = { "${meta.id}_snv_genmod_score" }
         ext.args = "--rank_results"
     }
-
     withName: '.*:RANK_VARIANTS_SNV:GENMOD_COMPOUND' {
         ext.prefix = { "${meta.id}_snv_genmod_compound" }
         ext.args = "--temp_dir ./"
     }
 
+    //
+    // Score and rank SVSs
+    //
+    withName: '.*:RANK_VARIANTS_SVS:.*' {
+        publishDir = [
+            enabled: false,
+        ]
+    }
+    withName: '.*:RANK_VARIANTS_SVS:GENMOD_ANNOTATE' {
+        ext.prefix = { "${meta.id}_svs_genmod_annotate" }
+        ext.args = { [
+            '--annotate_regions',
+            '--genome-build 38',
+            '--temp_dir ./'
+            ].join(' ') }
+    }
+    withName: '.*:RANK_VARIANTS_SVS:GENMOD_MODELS' {
+        ext.prefix = { "${meta.id}_svs_genmod_models" }
+        ext.args = "--whole_gene --temp_dir ./"
+    }
+    withName: '.*:RANK_VARIANTS_SVS:GENMOD_SCORE' {
+        ext.prefix = { "${meta.id}_svs_genmod_score" }
+        ext.args = "--rank_results"
+    }
+    withName: '.*:RANK_VARIANTS_SVS:GENMOD_COMPOUND' {
+        ext.prefix = { "${meta.id}_svs_genmod_compound" }
+        ext.args = "--temp_dir ./"
+    }
+    withName: '.*:RANK_VARIANTS_SVS:TABIX_BGZIPTABIX' {
+        ext.prefix = { params.skip_cnv_calling ? "${meta.id}_svs_merged_annotated_ranked" : "${meta.id}_svs_cnvs_merged_annotated_ranked" }
+        publishDir = [
+            path: { "${params.outdir}/svs/family/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 }
diff --git a/conf/modules/short_variant_calling.config b/conf/modules/short_variant_calling.config
@@ -43,6 +43,14 @@ process {
             meta.sex == 1 ? '--haploid_contigs="chrX,chrY"' : ''
         ].join(' ') }
     }
+    withName: '.*:SHORT_VARIANT_CALLING:DEEPVARIANT_VCFSTATSREPORT' {
+        publishDir = [
+            path: { "${params.outdir}/qc/deepvariant_vcfstatsreport/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+
+    }
 
     withName: '.*:SHORT_VARIANT_CALLING:GLNEXUS' {
         ext.args = '--config DeepVariant_unfiltered'
@@ -75,4 +83,5 @@ process {
             '-w 10000'
         ].join(' ')
     }
+
 }
diff --git a/conf/test.config b/conf/test.config
@@ -18,7 +18,7 @@ params {
     modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
 
     // Base directory for genomic-medicine-sweden/nallo test data
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/7be7114cb132be8cae9343f225bcf42ec11ecc1b/'
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/22fb5b8a1a358df96e49f8d01a9c6e18770fbd6d/'
 
     // References
     fasta                    = params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz'
@@ -36,7 +36,9 @@ params {
     svdb_dbs                 = params.pipelines_testdata_base_path + 'testdata/svdb_dbs.csv'
     reduced_penetrance       = params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv'
     score_config_snv         = params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini'
+    score_config_svs         = params.pipelines_testdata_base_path + 'reference/rank_model_svs.ini'
     variant_consequences_snv = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt'
+    variant_consequences_svs = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt'
     somalier_sites           = params.pipelines_testdata_base_path + 'reference/somalier_sites.vcf.gz'
 
     // Pipeline options