Merge branch 'main' into fix/ffpe-event-handling

snakemake-workflows · May 23, 2024 · c6f1265 · c6f1265
2 parents ae9c7ad + 98ef04b
commit c6f1265
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Showing 13 changed files with 136 additions and 48 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -51,7 +51,7 @@ jobs:
       with:
         directory: .test
         snakefile: workflow/Snakefile
-        args: "--configfile .test/config-tumor_normal/config.yaml --report report.zip"
+        args: "--configfile .test/config-tumor_normal/config.yaml --cores 1 --report report.zip"
 
     - name: Test workflow (tumor/normal, ffpe)
       uses: snakemake/snakemake-github-action@v1.24.0

diff --git a/.test/config-tumor_normal/config.yaml b/.test/config-tumor_normal/config.yaml
@@ -45,11 +45,18 @@ annotations:
   vep:
     # Consider removing --everything if VEP is slow for you (e.g. for WGS), 
     # and think carefully about which annotations you need.
-    params: --everything --check_existing
-    plugins:
-      # Add any plugin from https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
-      # Plugin args can be passed as well, e.g. "LoFtool,path/to/custom/scores.txt".
-      - LoFtool
+    candidate_calls:
+      params: --everything --check_existing
+      plugins:
+        # Add any plugin from https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
+        # Plugin args can be passed as well, e.g. "LoFtool,path/to/custom/scores.txt".
+        - LoFtool
+    final_calls:
+      params: --everything --check_existing
+      plugins:
+        # Add any plugin from https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
+        # Plugin args can be passed as well, e.g. "LoFtool,path/to/custom/scores.txt".
+        - LoFtool
 
 # printing of variants in a table format
 tables:

diff --git a/.test/config-tumor_normal/samples.tsv b/.test/config-tumor_normal/samples.tsv
@@ -1,3 +1,3 @@
-sample_name	group	alias	platform	purity	sex
-tumor	patient-a	tumor	ILLUMINA	0.89	female
-normal	patient-a	normal	ILLUMINA		female
+sample_name	group	alias	platform	purity	sex	datatype	calling
+tumor	patient-a	tumor	ILLUMINA	0.89	female	dna	variants
+normal	patient-a	normal	ILLUMINA		female	dna	variants
diff --git a/.test/config-tumor_normal_ffpe/config.yaml b/.test/config-tumor_normal_ffpe/config.yaml
@@ -45,11 +45,18 @@ annotations:
   vep:
     # Consider removing --everything if VEP is slow for you (e.g. for WGS), 
     # and think carefully about which annotations you need.
-    params: --everything --check_existing
-    plugins:
-      # Add any plugin from https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
-      # Plugin args can be passed as well, e.g. "LoFtool,path/to/custom/scores.txt".
-      - LoFtool
+    candidate_calls:
+      params: --everything --check_existing
+      plugins:
+        # Add any plugin from https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
+        # Plugin args can be passed as well, e.g. "LoFtool,path/to/custom/scores.txt".
+        - LoFtool
+    final_calls:
+      params: --everything --check_existing
+      plugins:
+        # Add any plugin from https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
+        # Plugin args can be passed as well, e.g. "LoFtool,path/to/custom/scores.txt".
+        - LoFtool
 
 # printing of variants in a table format
 tables:

diff --git a/.test/config-tumor_normal_ffpe/samples.tsv b/.test/config-tumor_normal_ffpe/samples.tsv
@@ -1,3 +1,3 @@
-sample_name	group	alias	platform	purity	sex	ffpe
-tumor	patient-a	tumor	ILLUMINA	0.89	female	1
-normal	patient-a	normal	ILLUMINA		female	0
+sample_name	group	alias	platform	purity	sex	ffpe	datatype	calling
+tumor	patient-a	tumor	ILLUMINA	0.89	female	1	dna	variants
+normal	patient-a	normal	ILLUMINA		female	0	dna	variants
diff --git a/.test/config-tumor_only/config.yaml b/.test/config-tumor_only/config.yaml
@@ -45,11 +45,18 @@ annotations:
   vep:
     # Consider removing --everything if VEP is slow for you (e.g. for WGS), 
     # and think carefully about which annotations you need.
-    params: --everything --check_existing
-    plugins:
-      # Add any plugin from https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
-      # Plugin args can be passed as well, e.g. "LoFtool,path/to/custom/scores.txt".
-      - LoFtool
+    candidate_calls:
+      params: --everything --check_existing
+      plugins:
+        # Add any plugin from https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
+        # Plugin args can be passed as well, e.g. "LoFtool,path/to/custom/scores.txt".
+        - LoFtool
+    final_calls:
+      params: --everything --check_existing
+      plugins:
+        # Add any plugin from https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
+        # Plugin args can be passed as well, e.g. "LoFtool,path/to/custom/scores.txt".
+        - LoFtool
 
 # printing of variants in a table format
 tables:

diff --git a/.test/config-tumor_only/samples.tsv b/.test/config-tumor_only/samples.tsv
@@ -1,2 +1,2 @@
-sample_name	group	alias	platform	purity	sex
-tumor	patient-a	tumor	ILLUMINA	0.89	male
+sample_name	group	alias	platform	purity	sex	datatype	calling
+tumor	patient-a	tumor	ILLUMINA	0.89	male	dna	variants
diff --git a/.test/config-tumor_only_ffpe/config.yaml b/.test/config-tumor_only_ffpe/config.yaml
@@ -45,11 +45,18 @@ annotations:
   vep:
     # Consider removing --everything if VEP is slow for you (e.g. for WGS), 
     # and think carefully about which annotations you need.
-    params: --everything --check_existing
-    plugins:
-      # Add any plugin from https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
-      # Plugin args can be passed as well, e.g. "LoFtool,path/to/custom/scores.txt".
-      - LoFtool
+    candidate_calls:
+      params: --everything --check_existing
+      plugins:
+        # Add any plugin from https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
+        # Plugin args can be passed as well, e.g. "LoFtool,path/to/custom/scores.txt".
+        - LoFtool
+    final_calls:
+      params: --everything --check_existing
+      plugins:
+        # Add any plugin from https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
+        # Plugin args can be passed as well, e.g. "LoFtool,path/to/custom/scores.txt".
+        - LoFtool
 
 # printing of variants in a table format
 tables:

diff --git a/.test/config-tumor_only_ffpe/samples.tsv b/.test/config-tumor_only_ffpe/samples.tsv
@@ -1,2 +1,2 @@
-sample_name	group	alias	platform	purity	sex	ffpe
-tumor	patient-a	tumor	ILLUMINA	0.89	male	1
+sample_name	group	alias	platform	purity	sex	ffpe	datatype	calling
+tumor	patient-a	tumor	ILLUMINA	0.89	male	1	dna	variants
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,39 @@
 # Changelog
 
+### [1.6.2](https://www.github.com/snakemake-workflows/dna-seq-mtb/compare/v1.6.1...v1.6.2) (2024-03-26)
+
+
+### Bug Fixes
+
+* update to dna-seq-varlociraptor 5.4.0 ([#42](https://www.github.com/snakemake-workflows/dna-seq-mtb/issues/42)) ([a2f9923](https://www.github.com/snakemake-workflows/dna-seq-mtb/commit/a2f9923a096614533565b73b8bddadd7e654be5f))
+
+### [1.6.1](https://www.github.com/snakemake-workflows/dna-seq-mtb/compare/v1.6.0...v1.6.1) (2024-03-13)
+
+
+### Bug Fixes
+
+* update to dna-seq-varlociraptor 5.3.1 ([#39](https://www.github.com/snakemake-workflows/dna-seq-mtb/issues/39)) ([5c5994b](https://www.github.com/snakemake-workflows/dna-seq-mtb/commit/5c5994bb875b282daa7216f27ed2c067e9832c04))
+
+## [1.6.0](https://www.github.com/snakemake-workflows/dna-seq-mtb/compare/v1.5.0...v1.6.0) (2024-03-05)
+
+
+### Features
+
+* support dna-seq-varlociraptor 5.3.0 ([#37](https://www.github.com/snakemake-workflows/dna-seq-mtb/issues/37)) ([366f76c](https://www.github.com/snakemake-workflows/dna-seq-mtb/commit/366f76c44e212a56e7462e899def0aaa4e8cf18d))
+
+## [1.5.0](https://www.github.com/snakemake-workflows/dna-seq-mtb/compare/v1.4.1...v1.5.0) (2024-02-09)
+
+
+### Features
+
+* add callset consisting of all found variants ([a436c97](https://www.github.com/snakemake-workflows/dna-seq-mtb/commit/a436c97fe95a97ee683a1b00af39c455b53ba4b5))
+* update config ([#36](https://www.github.com/snakemake-workflows/dna-seq-mtb/issues/36)) ([6621515](https://www.github.com/snakemake-workflows/dna-seq-mtb/commit/6621515558cc736c867e58b071845233e79d7ed5))
+
+
+### Bug Fixes
+
+* set lowercase column names ([#31](https://www.github.com/snakemake-workflows/dna-seq-mtb/issues/31)) ([de1f5c3](https://www.github.com/snakemake-workflows/dna-seq-mtb/commit/de1f5c31ccde8780592dfdbc4788beefd0675f8c))
+
 ### [1.4.1](https://www.github.com/snakemake-workflows/dna-seq-mtb/compare/v1.4.0...v1.4.1) (2023-05-08)
 
 

diff --git a/config/samples.tsv b/config/samples.tsv
@@ -1 +1 @@
-sample_name	alias	group	platform	purity	panel	sex	ffpe
+sample_name	alias	group	platform	purity	panel	sex	ffpe	datatype	calling
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -6,7 +6,7 @@ module dna_seq_varlociraptor:
         github(
             "snakemake-workflows/dna-seq-varlociraptor",
             path="workflow/Snakefile",
-            tag="v4.0.1",
+            tag="v5.6.0",
         )
     config:
         config

diff --git a/workflow/resources/config/default.yaml b/workflow/resources/config/default.yaml
@@ -29,7 +29,7 @@ ref:
   # Ensembl species name
   species: homo_sapiens
   # Ensembl release
-  release: 109
+  release: 111
   # Genome build
   build: GRCh38
 
@@ -58,6 +58,12 @@ mutational_burden:
     - somatic_tumor_low
     - somatic_tumor_high
 
+# Sets the minimum average coverage for each gene.
+# Genes with lower average coverage will not be concidered in gene coverage datavzrd report
+# If not present min_avg_coverage will be set to 0 rendering all genes.
+gene_coverage:
+  min_avg_coverage: 5
+
 # printing of variants in a matrix, sorted by recurrence
 report:
   # if stratificatio is deactivated, one oncoprint for all
@@ -108,13 +114,13 @@ calling:
     novel: >-
       not (ID and ID.startswith('rs'))
     pathogenic_risk_factor_drug_response: >-
-      (not {'risk_factor', 'pathogenic', 'drug_response'}.isdisjoint(ANN['CLIN_SIG'])) and 
-      (ANN['IMPACT'] in {'LOW', 'MODERATE', 'HIGH'})
+      (not {'risk_factor','pathogenic', 'drug_response'}.isdisjoint(ANN['CLIN_SIG'])) and 
+      (ANN['IMPACT'] in {'LOW', 'MODERATE', 'HIGH'}) and (ANN['REVEL'] is NA or ANN['REVEL'] >= 0.5)
     potentially_pathogenic: >-
       (ANN['IMPACT'] in {'LOW', 'MODERATE', 'HIGH'}) and (
       ((not {'risk_factor', 'pathogenic', 'drug_response'}.isdisjoint(ANN['CLIN_SIG'])) and ANN['REVEL'] is not NA and ANN['REVEL'] < 0.5) or (
-      'likely_pathogenic' in ANN['CLIN_SIG'] and not (
-      (not {'risk_factor', 'pathogenic', 'drug_response'}.isdisjoint(ANN['CLIN_SIG'])) and ANN['REVEL'] is NA or ANN['REVEL'] >= 0.5)))
+      'likely_pathogenic' in ANN['CLIN_SIG'] and (
+      ({'risk_factor', 'pathogenic', 'drug_response'}.isdisjoint(ANN['CLIN_SIG'])) and (ANN['REVEL'] is NA or ANN['REVEL'] >= 0.5))))
     loh_relevant: >-
       ANN['IMPACT'] != 'LOW' and ANN['IMPACT'] != 'MODIFIER' and
       not (set(["benign", "likely benign"]) > set(ANN['CLIN_SIG']) and "benign" in ANN['CLIN_SIG'])
@@ -158,6 +164,7 @@ calling:
     events:
       ?for event_type in ["somatic_or_germline", "loh"]:
         ?f"{event_type}_impact_moderate_novel":
+          types: ["variants"]
           varlociraptor: ?get_events(event_type)
           filter:
             - impact_moderate
@@ -175,6 +182,7 @@ calling:
           subcategory: ?get_description(event_type)
 
         ?f"{event_type}_impact_high_novel":
+          types: ["variants"]
           varlociraptor: ?get_events(event_type)
           filter:
             - impact_high
@@ -191,8 +199,9 @@ calling:
             impact: high
           subcategory: ?get_description(event_type)
 
-        ? ?f"{event_type}_pathogenic_risk_factor_drug_response"
-        : varlociraptor: ?get_events(event_type, include_ffpe=True)
+        ?f"{event_type}_pathogenic_risk_factor_drug_response":
+          types: ["variants"]
+          varlociraptor: ?get_events(event_type, include_ffpe=True)
           filter:
             - pathogenic_risk_factor_drug_response
             - revel_malign
@@ -208,8 +217,9 @@ calling:
             impact: low, moderate, high
           subcategory: ?get_description(event_type)
 
-        ? ?f"{event_type}_potentially_pathogenic_risk_factor_drug_response"
-        : varlociraptor: ?get_events(event_type, include_ffpe=True)
+        ?f"{event_type}_potentially_pathogenic_risk_factor_drug_response":
+          types: ["variants"]
+          varlociraptor: ?get_events(event_type, include_ffpe=True)
           filter:
             - potentially_pathogenic
           sort:
@@ -225,6 +235,7 @@ calling:
           subcategory: ?get_description(event_type)
 
         ?f"{event_type}_splice_variants":
+          types: ["variants"]
           varlociraptor: ?get_events(event_type)
           filter:
             - splice_mutation
@@ -241,6 +252,7 @@ calling:
           subcategory: ?get_description(event_type)
 
         ?f"{event_type}_cancer_genes":
+          types: ["variants"]
           varlociraptor: ?get_events(event_type)
           filter:
             - cancer_relevant
@@ -256,6 +268,7 @@ calling:
           subcategory: ?get_description(event_type)
 
         ?f"{event_type}_pi3k_pathway":
+          types: ["variants"]
           varlociraptor: ?get_events(event_type)
           filter:
             - cancer_relevant
@@ -272,6 +285,7 @@ calling:
           subcategory: ?get_description(event_type)
 
         ?f"{event_type}_raf_pathway":
+          types: ["variants"]
           varlociraptor: ?get_events(event_type)
           filter:
             - cancer_relevant
@@ -288,6 +302,7 @@ calling:
           subcategory: ?get_description(event_type)
 
         ?f"{event_type}_cell_cycle":
+          types: ["variants"]
           varlociraptor: ?get_events(event_type)
           filter:
             - cancer_relevant
@@ -304,6 +319,7 @@ calling:
           subcategory: ?get_description(event_type)
 
         ?f"{event_type}_dna_damage_response":
+          types: ["variants"]
           varlociraptor: ?get_events(event_type)
           filter:
             - cancer_relevant
@@ -320,6 +336,7 @@ calling:
           subcategory: ?get_description(event_type)
 
         ?f"{event_type}_g1_topart":
+          types: ["variants"]
           varlociraptor: ?get_events(event_type)
           filter:
             - cancer_relevant
@@ -336,6 +353,7 @@ calling:
           subcategory: ?get_description(event_type)
 
         ?f"{event_type}_tyrosine_kinases":
+          types: ["variants"]
           varlociraptor: ?get_events(event_type)
           filter:
             - cancer_relevant
@@ -377,12 +395,20 @@ annotations:
   vep:
     # Consider removing --everything if VEP is slow for you (e.g. for WGS),
     # and think carefully about which annotations you need.
-    params: --everything --check_existing
-    plugins:
-      # Add any plugin from https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
-      # Plugin args can be passed as well, e.g. "LoFtool,path/to/custom/scores.txt".
-      - LoFtool
-      - REVEL
+    candidate_calls:
+      params: --everything --check_existing
+      plugins:
+        # Add any plugin from https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
+        # Plugin args can be passed as well, e.g. "LoFtool,path/to/custom/scores.txt".
+        - LoFtool
+        - REVEL
+    final_calls:
+      params: --everything --check_existing
+      plugins:
+        # Add any plugin from https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
+        # Plugin args can be passed as well, e.g. "LoFtool,path/to/custom/scores.txt".
+        - LoFtool
+        - REVEL
 
 params:
   cutadapt: ""