From a5264b7d36b9b26943ea29e700eec33a52033106 Mon Sep 17 00:00:00 2001 From: Mark Walker Date: Tue, 14 Jan 2025 10:33:55 -0500 Subject: [PATCH] Address comments --- .../GATKSVPipelineSingleSample.json.tmpl | 1 - .../04_variant_resolution/scripts/reformat_genotyped_vcf.py | 1 - src/sv-pipeline/scripts/format_gatk_vcf_for_svtk.py | 4 +--- wdl/CombineBatches.wdl | 2 +- wdl/GenotypeBatch.wdl | 4 ---- wdl/GenotypeDepthPart2.wdl | 2 -- wdl/GenotypePESRPart2.wdl | 2 -- 7 files changed, 2 insertions(+), 14 deletions(-) diff --git a/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl b/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl index b020837bb..b4b33bed3 100644 --- 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 index 3c2c510bc..fe7034ae3 100644 --- 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 index 768267c5f..43755c74b 100644 --- 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 index d1b432024..825a59137 100644 --- 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 index c78a4f7eb..04343733c 100644 --- 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 index 8415008ef..579149fa2 100644 --- 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 index a3a652971..80b45d061 100644 --- 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