fix: write out pedigrees was missing for sv_calling_wgs (#379)

bihealth · Feb 22, 2023 · 573c72f · 573c72f
1 parent 6d95d88
commit 573c72f
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Showing 3 changed files with 18 additions and 1 deletion.
diff --git a/snappy_pipeline/workflows/common/gcnv/gcnv_run.py b/snappy_pipeline/workflows/common/gcnv/gcnv_run.py
@@ -258,6 +258,12 @@ def _get_input_files_contig_ploidy(self, wildcards: Wildcards):
                 name_pattern = f"{wildcards.mapper}.gcnv_coverage.{lib}"
                 tsvs.append(f"work/{name_pattern}/out/{name_pattern}.{ext}")
         yield ext, tsvs
+        # Yield path to pedigree file
+        peds = []
+        for library_name in sorted(self.index_ngs_library_to_pedigree):
+            name_pattern = f"write_pedigree.{library_name}"
+            peds.append(f"work/{name_pattern}/out/{library_name}.ped")
+        yield "ped", peds
 
     @dictify
     def _get_output_files_contig_ploidy(self):

diff --git a/snappy_pipeline/workflows/sv_calling_wgs/Snakefile b/snappy_pipeline/workflows/sv_calling_wgs/Snakefile
@@ -28,6 +28,11 @@ wf = SvCallingWgsWorkflow(workflow, config, lookup_paths, config_paths, os.getcw
 # Rules =======================================================================
 
 
+localrules:
+    # Writing out pedigrees can be done locally
+    sv_calling_wgs_write_pedigree_run,
+
+
 rule all:
     input:
         wf.get_result_files(),

diff --git a/tests/snappy_pipeline/workflows/test_workflows_sv_calling_targeted.py b/tests/snappy_pipeline/workflows/test_workflows_sv_calling_targeted.py
@@ -633,7 +633,13 @@ def test_gcnv_contig_ploidy_step_part_get_input_files(sv_calling_targeted_workfl
         "work/bwa.gcnv_coverage.P00{i}-N1-DNA1-WGS1/out/bwa.gcnv_coverage.P00{i}-N1-DNA1-WGS1.tsv"
     )
     tsv_list_out = [tsv_pattern.format(i=i) for i in range(1, 7)]  # P001 - P006
-    expected = {"tsv": tsv_list_out}
+    expected = {
+        "tsv": tsv_list_out,
+        "ped": [
+            "work/write_pedigree.P001-N1-DNA1-WGS1/out/P001-N1-DNA1-WGS1.ped",
+            "work/write_pedigree.P004-N1-DNA1-WGS1/out/P004-N1-DNA1-WGS1.ped",
+        ],
+    }
     # Get actual
     wildcards = Wildcards(
         fromdict={"mapper": "bwa", "library_kit": "Agilent_SureSelect_Human_All_Exon_V6"}