Updated WDL input params

broadinstitute · Nov 25, 2024 · cce70ae · cce70ae
1 parent 9c457d1
commit cce70ae
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 8 deletions.
diff --git a/src/sv-pipeline/scripts/make_evidence_qc_table.py b/src/sv-pipeline/scripts/make_evidence_qc_table.py
@@ -222,7 +222,7 @@ def merge_evidence_qc_table(
     df_melt_insert_size = read_melt_insert_size(filename_melt_insert_size)
 
     # outlier column names
-    callers = ["wham", "melt", "manta", "scramble", "overall"]
+    callers = ["wham", "melt", "manta", "scramble", "dragen", "overall"]
     types = ["high", "low"]
     outlier_cols = [get_col_name(caller, type) for caller in callers for type in types]
 

diff --git a/wdl/MakeGqRecalibratorTrainingSetFromPacBio.wdl b/wdl/MakeGqRecalibratorTrainingSetFromPacBio.wdl
@@ -12,7 +12,6 @@ workflow MakeGqRecalibratorTrainingSetFromPacBio {
     # SVConcordance should be run first if the training set is a proper subset of the cohort
     # This can be either a single whole-genome vcf or multiple vcf shards.
     # Assumes all vcfs have indexes, i.e. at {VCF_PATH}.tbi
-    # Test comment
     Array[File] vcfs
 
     File training_sample_ids  # Sample IDs with PacBio or array data
@@ -66,14 +65,10 @@ workflow MakeGqRecalibratorTrainingSetFromPacBio {
   ])
 
   Array[Array[File]] tool_vcfs_list = select_all([pbsv_vcfs, pav_vcfs, sniffles_vcfs, hifi_cnv_vcfs, hapdiff_vcfs])
-  
+
   Array[Array[File]] pacbio_vcfs = transpose(tool_vcfs_list)
 
-  String output_prefix_ =
-    if defined(output_prefix) then
-      select_first([output_prefix])
-    else
-        basename(vcfs[0], ".vcf.gz")
+  String output_prefix_ = if defined(output_prefix) then select_first([output_prefix]) else basename(vcfs[0], ".vcf.gz")
 
   scatter (i in range(length(vcfs))) {
     call utils.SubsetVcfBySamplesList as SubsetTrainingSamples {