Address comments

broadinstitute · Jan 14, 2025 · a5264b7 · a5264b7
1 parent f889c50
commit a5264b7
Show file tree

Hide file tree

Showing 7 changed files with 2 additions and 14 deletions.
diff --git a/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl b/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl
@@ -31,7 +31,6 @@
 
   "GATKSVPipelineSingleSample.linux_docker" : {{ dockers.linux_docker | tojson }},
   "GATKSVPipelineSingleSample.manta_docker": {{ dockers.manta_docker | tojson }},
-  "GATKSVPipelineSingleSample.melt_docker": {{ dockers.melt_docker | tojson }},
   "GATKSVPipelineSingleSample.scramble_docker": {{ dockers.scramble_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_base_docker": {{ dockers.sv_base_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/reformat_genotyped_vcf.py b/src/sv-pipeline/04_variant_resolution/scripts/reformat_genotyped_vcf.py
@@ -44,7 +44,6 @@ def get_new_header(header):
             continue
         else:
             new_header_lines.append(line)
-    # Incorporate SR evidence flags
     new_header = pysam.VariantHeader()
     for s in header.samples:
         new_header.add_sample(s)

diff --git a/src/sv-pipeline/scripts/format_gatk_vcf_for_svtk.py b/src/sv-pipeline/scripts/format_gatk_vcf_for_svtk.py
@@ -197,7 +197,7 @@ def __parse_arg_list(arg: Text) -> List[Text]:
 def __parse_arguments(argv: List[Text]) -> argparse.Namespace:
     # noinspection PyTypeChecker
     parser = argparse.ArgumentParser(
-        description="Convert a GATK-style SV VCF from ClusterBatch for consumption by GenerateBatchMetrics.",
+        description="Convert a GATK-style SV VCF for consumption by svtk. Not to be used after CleanVcf.",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter
     )
     parser.add_argument("--vcf", type=str, required=True,
@@ -212,8 +212,6 @@ def __parse_arguments(argv: List[Text]) -> argparse.Namespace:
                         help="Comma-delimited list of FORMAT fields to remove")
     parser.add_argument("--remove-infos", type=str,
                         help="Comma-delimited list of INFO fields to remove")
-    parser.add_argument("--intervaled-ins", default=False, action='store_true',
-                        help="Set INS record END to POS+SVLEN")
     parser.add_argument("--set-pass", default=False, action='store_true',
                         help="Set empty FILTER fields (\".\") to PASS")
     if len(argv) <= 1:

diff --git a/wdl/CombineBatches.wdl b/wdl/CombineBatches.wdl
@@ -125,7 +125,7 @@ workflow CombineBatches {
   Array[String] contigs = transpose(read_tsv(contig_list))[0]
   scatter ( contig in contigs ) {
 
-    # First round of clustering
+    # Naively join across batches
     call ClusterTasks.SVCluster as JoinVcfs {
       input:
         vcfs=FormatVcf.out,

diff --git a/wdl/GenotypeBatch.wdl b/wdl/GenotypeBatch.wdl
@@ -50,8 +50,6 @@ workflow GenotypeBatch {
     Int? sr_median_hom_ins
     Float? sr_hom_cutoff_multiplier
 
-    File? reformat_script
-
     String sv_base_mini_docker
     String sv_pipeline_docker
     String linux_docker
@@ -192,7 +190,6 @@ workflow GenotypeBatch {
       ref_dict = ref_dict,
       sr_hom_cutoff_multiplier = sr_hom_cutoff_multiplier,
       sr_median_hom_ins = sr_median_hom_ins,
-      reformat_script = reformat_script,
       sv_base_mini_docker = sv_base_mini_docker,
       sv_pipeline_docker = sv_pipeline_docker,
       linux_docker = linux_docker,
@@ -251,7 +248,6 @@ workflow GenotypeBatch {
       coveragefile_index = coveragefile_index,
       n_per_split = n_per_split,
       ref_dict = ref_dict,
-      reformat_script = reformat_script,
       sv_base_mini_docker = sv_base_mini_docker,
       sv_pipeline_docker = sv_pipeline_docker,
       runtime_attr_split_variants = runtime_attr_split_variants,

diff --git a/wdl/GenotypeDepthPart2.wdl b/wdl/GenotypeDepthPart2.wdl
@@ -20,8 +20,6 @@ workflow GenotypeDepthPart2 {
     File coveragefile
     File? coveragefile_index
 
-    File? reformat_script
-
     String sv_pipeline_docker
     String sv_base_mini_docker
     RuntimeAttr? runtime_attr_split_variants

diff --git a/wdl/GenotypePESRPart2.wdl b/wdl/GenotypePESRPart2.wdl
@@ -31,8 +31,6 @@ workflow GenotypePESRPart2 {
     Int? sr_median_hom_ins
     Float? sr_hom_cutoff_multiplier
 
-    File? reformat_script
-
     String sv_pipeline_docker
     String sv_base_mini_docker
     String linux_docker