feat: updated biomarker module for optitype

config/config.yaml

@@ -268,7 +268,7 @@ multiqc:
 
 optitype:
   #container: "docker://hydragenetics/optitype:1.3.5"
-  container: "docker://fred2/optitype"
+  container: "docker://fred2/optitype:release-v1.3.1"
   sample_type: "-d"
   enumeration: 4
 

config/output_files.yaml

@@ -407,3 +407,15 @@ files:
     output: results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.manta_tumorSV.vcf.gz
     types:
       - T
+  - name: HLA optitype
+    input: biomarker/optitype/{sample}_{type}/{sample}_{type}_hla_type_result.tsv
+    output: results/dna/hla/{sample}_{type}_hla_type_result.tsv
+    types:
+      - T
+      - N
+  - name: HLA coverage optitype
+    input: biomarker/optitype/{sample}_{type}/{sample}_{type}_hla_type_coverage_plot.pdf
+    output: results/dna/hla/{sample}_{type}_hla_type_coverage_plot.pdf
+    types:
+      - T
+      - N

workflow/Snakefile

@@ -414,7 +414,7 @@ use rule gatk_get_pileup_summaries from qc as qc_gatk_get_pileup_summaries with:
 
 module biomarker:
     snakefile:
-        get_module_snakefile(config, "hydra-genetics/biomarker", path="workflow/Snakefile", tag="v0.4.0")
+        get_module_snakefile(config, "hydra-genetics/biomarker", path="workflow/Snakefile", tag="8a20b04")
     config:
         config
 

workflow/schemas/singularity.schema.yaml

@@ -268,7 +268,7 @@ properties:
         type: string
         description: name or path to a default docker/singularity container
         pattern: >-
-            fred2/optitype$|fred2_optitype\.sif$
+            fred2/optitype:release-v1\.3\.1$|fred2_optitype_release-v1\.3\.1\.sif$
       required:
         - container