merge conflicts outputs snippy tidy up

theiagen · Oct 7, 2024 · 747f5aa · 747f5aa
1 parent 2029694
commit 747f5aa
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Showing 2 changed files with 2 additions and 3 deletions.
diff --git a/tasks/gene_typing/variant_detection/task_snippy_variants.wdl b/tasks/gene_typing/variant_detection/task_snippy_variants.wdl
@@ -149,6 +149,8 @@ task snippy_variants {
     String snippy_variants_ref_length = read_string("REFERENCE_LENGTH")
     String snippy_variants_ref_length_passed_depth = read_string("REFERENCE_LENGTH_PASSED_DEPTH")
     String snippy_variants_percent_ref_coverage = read_string("PERCENT_REF_COVERAGE")
+    File snippy_variants_qc_metrics = "~{samplename}/~{samplename}_qc_metrics.tsv"
+    String snippy_variants_percent_reads_aligned = read_string("PERCENT_READS_ALIGNED")
   }
   runtime {
       docker: "~{docker}"

diff --git a/workflows/standalone_modules/wf_snippy_variants.wdl b/workflows/standalone_modules/wf_snippy_variants.wdl
@@ -70,11 +70,8 @@ workflow snippy_variants_wf {
     File snippy_variants_coverage_tsv = snippy_variants.snippy_variants_coverage_tsv
     Int snippy_variants_num_variants = snippy_variants.snippy_variants_num_variants
     Float snippy_variants_percent_ref_coverage = snippy_variants.snippy_variants_percent_ref_coverage
-<<<<<<< HEAD
     File snippy_variants_qc_metrics = snippy_variants.snippy_variants_qc_metrics
-=======
     Float snippy_variants_percent_reads_aligned  = snippy_variants.snippy_variants_percent_reads_aligned
->>>>>>> main
     # snippy gene query outputs
     String? snippy_variants_query = snippy_gene_query.snippy_variants_query
     String? snippy_variants_query_check = snippy_gene_query.snippy_variants_query_check