Update WDLs to adhere with miniwdl validation (broadinstitute#439)

* Bug fix. * Remove duplicate arg declaration. * The workflow does not have the contig arg. * Add the missing required value. * Deleted a commented-out arg.
yuliamostovoy · Oct 7, 2022 · 46c5546 · 46c5546
1 parent f0118c9
commit 46c5546
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Showing 3 changed files with 5 additions and 6 deletions.
diff --git a/scripts/test/miniwdl_validation.py b/scripts/test/miniwdl_validation.py
@@ -42,8 +42,7 @@ def check(wdl_filename, imports_dir, import_max_depth):
             f"maximum {import_max_depth} import depth. You may separately check the "
             f"WDLs imported in {wdl_filename} and make sure they all pass the "
             f"miniwdl validation."))
-    finally:
-        return False
+    return False
 
 
 def main():

diff --git a/wdl/CalcAF.wdl b/wdl/CalcAF.wdl
@@ -16,7 +16,6 @@ workflow CalcAF {
     File? famfile                 #Used for M/F AF calculations
     File? par_bed                 #Used for marking hemizygous males on X & Y
     File? allosomes_list          #allosomes .fai used to override default sex chromosome assignments
-    String sv_pipeline_docker
     String? drop_empty_records
 
     RuntimeAttr? runtime_attr_compute_shard_af

diff --git a/wdl/prune_add_af.wdl b/wdl/prune_add_af.wdl
@@ -10,14 +10,15 @@ workflow prune_and_add_vafs {
     File vcf_idx
     String prefix
     String sv_pipeline_docker
+    String sv_pipeline_updates_docker
 
     File? sample_pop_assignments  #Two-column file with sample ID & pop assignment. "." for pop will ignore sample
     File? prune_list              #List of samples to be excluded from the output vcf
     File? famfile                 #Used for M/F AF calculations
     File? par_bed                 #Used to mark hemizygous males on chrX/Y
     Int sv_per_shard
     File contiglist
-    String? drop_empty_records  
+    String? drop_empty_records
 
   }
   Array[Array[String]] contigs=read_tsv(contiglist)
@@ -38,14 +39,14 @@ workflow prune_and_add_vafs {
       input:
         vcf=PruneVcf.pruned_vcf,
         vcf_idx=PruneVcf.pruned_vcf_idx,
-        contig=contig[0],
         sv_per_shard=sv_per_shard,
         prefix=prefix,
         sample_pop_assignments=sample_pop_assignments,
         famfile=famfile,
         par_bed=par_bed,
         drop_empty_records=drop_empty_records,
-        sv_pipeline_docker=sv_pipeline_docker
+        sv_pipeline_docker=sv_pipeline_docker,
+        sv_pipeline_updates_docker=sv_pipeline_updates_docker
     }
   }