Merge pull request #63 from genomic-medicine-sweden/handle_sample_types

feat: only run pgx on specific sample types

config/output_files.yaml

@@ -2,15 +2,27 @@ files:
   - name: "_copy_detected_variants"
     input: "pgx/detected_variants/{sample}_{type}.annotated.csv"
     output: "results/dna/additional_files/pgx/{sample}_{type}.detected_variants.csv"
+    types:
+      - T
+      - N
 
   - name: "_copy_depth_of_baits"
     input: "pgx/depth_of_coverage/depth_of_baits/{sample}_{type}.output.gdf"
     output: "results/dna/additional_files/pgx/{sample}_{type}.depth_of_baits.gdf"
+    types:
+      - T
+      - N
 
   - name: "_copy_depth_at_missing"
     input: "pgx/append_id_to_gdf/{sample}_{type}.depth_at_missing_annotated.gdf"
     output: "results/dna/additional_files/pgx/{sample}_{type}.depth_at_missing_annotated.gdf"
+    types:
+      - T
+      - N
 
   - name: "_copy_pgx_report"
     input: "pgx/generate_pgx_report/{sample}_{type}_pgx_report.txt"
     output: "results/dna/pgx/{sample}_{type}.pgx_report.txt"
+    types:
+      - T
+      - N

workflow/rules/common.smk

@@ -75,6 +75,7 @@ wildcard_constraints:
 def compile_output_file_list(wildcards):
     outdir = pathlib.Path(output_spec.get("directory", "./"))
     output_files = []
+    types = set([unit.type for unit in units.itertuples()])
 
     for f in output_spec["files"]:
         # Please remember to add any additional values down below
@@ -84,6 +85,7 @@ def compile_output_file_list(wildcards):
                 f["output"].format(sample=sample, type=unit_type)
                 for sample in get_samples(samples)
                 for unit_type in get_unit_types(units, sample)
+                if unit_type in set(f["types"]).intersection(types)
             ]
         )
         for op in outputpaths: