From 45504d6e8228573efe56cbacc7d33539fb342612 Mon Sep 17 00:00:00 2001 From: Malachi Griffith Date: Tue, 11 Apr 2023 15:58:48 -0500 Subject: [PATCH 01/10] make use of var frequency variables more consistent --- definitions/detect_variants.wdl | 19 +++++++++++------- definitions/detect_variants_nonhuman.wdl | 19 +++++++++++------- definitions/detect_variants_wgs.wdl | 20 +++++++++++-------- definitions/immuno.wdl | 11 ++++++---- definitions/somatic_exome.wdl | 11 ++++++---- definitions/somatic_exome_cle.wdl | 10 ++++++---- definitions/somatic_exome_nonhuman.wdl | 11 ++++++---- definitions/somatic_wgs.wdl | 11 +++++----- definitions/subworkflows/fp_filter.wdl | 4 ++-- definitions/subworkflows/mutect.wdl | 4 +++- definitions/subworkflows/pindel.wdl | 4 +++- .../strelka_and_post_processing.wdl | 5 ++++- definitions/subworkflows/varscan.wdl | 11 +++++----- .../varscan_pre_and_post_processing.wdl | 13 ++++++------ definitions/tools/fp_filter.wdl | 4 ++-- definitions/tools/varscan_somatic.wdl | 8 ++++---- definitions/tumor_only_detect_variants.wdl | 10 +++++----- definitions/tumor_only_exome.wdl | 10 +++++----- definitions/tumor_only_wgs.wdl | 6 +++--- 19 files changed, 112 insertions(+), 79 deletions(-) diff --git a/definitions/detect_variants.wdl b/definitions/detect_variants.wdl index fb334f51..591bcf2f 100644 --- a/definitions/detect_variants.wdl +++ b/definitions/detect_variants.wdl @@ -36,12 +36,14 @@ workflow detectVariants { Boolean strelka_exome_mode Int strelka_cpu_reserved = 8 - Int varscan_strand_filter = 0 - Int varscan_min_coverage = 8 - Float varscan_min_var_freq = 0.1 - Float varscan_p_value = 0.99 + Int varscan_strand_filter + Int varscan_min_coverage + Float varscan_min_var_freq + Float varscan_p_value Float? varscan_max_normal_freq + Float fp_min_var_freq + File docm_vcf File docm_vcf_tbi @@ -89,7 +91,8 @@ workflow detectVariants { normal_bam=normal_bam, normal_bam_bai=normal_bam_bai, interval_list=roi_intervals, - scatter_count=scatter_count + scatter_count=scatter_count, + fp_min_var_freq=fp_min_var_freq } call sapp.strelkaAndPostProcessing as strelka { @@ -105,7 +108,8 @@ workflow detectVariants { exome_mode=strelka_exome_mode, cpu_reserved=strelka_cpu_reserved, normal_sample_name=normal_sample_name, - tumor_sample_name=tumor_sample_name + tumor_sample_name=tumor_sample_name, + fp_min_var_freq=fp_min_var_freq } call vpapp.varscanPreAndPostProcessing as varscan { @@ -121,9 +125,10 @@ workflow detectVariants { scatter_count=scatter_count, strand_filter=varscan_strand_filter, min_coverage=varscan_min_coverage, - min_var_freq=varscan_min_var_freq, + varscan_min_var_freq=varscan_min_var_freq, p_value=varscan_p_value, max_normal_freq=varscan_max_normal_freq, + fp_min_var_freq=fp_min_var_freq, normal_sample_name=normal_sample_name, tumor_sample_name=tumor_sample_name } diff --git a/definitions/detect_variants_nonhuman.wdl b/definitions/detect_variants_nonhuman.wdl index 765c419c..5b79d780 100644 --- a/definitions/detect_variants_nonhuman.wdl +++ b/definitions/detect_variants_nonhuman.wdl @@ -33,12 +33,14 @@ workflow detectVariantsNonhuman { Boolean strelka_exome_mode Int strelka_cpu_reserved = 8 - Int varscan_strand_filter = 0 - Int varscan_min_coverage = 8 - Float varscan_min_var_freq = 0.1 - Float varscan_p_value = 0.99 + Int varscan_strand_filter + Int varscan_min_coverage + Float varscan_min_var_freq + Float varscan_p_value Float? varscan_max_normal_freq + Float fp_min_var_freq + File vep_cache_dir_zip String vep_ensembl_assembly String vep_ensembl_version @@ -74,7 +76,8 @@ workflow detectVariantsNonhuman { normal_bam=normal_bam, normal_bam_bai=normal_bam_bai, interval_list=roi_intervals, - scatter_count=scatter_count + scatter_count=scatter_count, + fp_min_var_freq=fp_min_var_freq } call sapp.strelkaAndPostProcessing as strelka { @@ -90,7 +93,8 @@ workflow detectVariantsNonhuman { exome_mode=strelka_exome_mode, cpu_reserved=strelka_cpu_reserved, normal_sample_name=normal_sample_name, - tumor_sample_name=normal_sample_name + tumor_sample_name=normal_sample_name, + fp_min_var_freq=fp_min_var_freq } call vpapp.varscanPreAndPostProcessing as varscan { @@ -106,9 +110,10 @@ workflow detectVariantsNonhuman { scatter_count=scatter_count, strand_filter=varscan_strand_filter, min_coverage=varscan_min_coverage, - min_var_freq=varscan_min_var_freq, + varscan_min_var_freq=varscan_min_var_freq, p_value=varscan_p_value, max_normal_freq=varscan_max_normal_freq, + fp_min_var_freq=fp_min_var_freq, normal_sample_name=normal_sample_name, tumor_sample_name=tumor_sample_name } diff --git a/definitions/detect_variants_wgs.wdl b/definitions/detect_variants_wgs.wdl index ce2142ef..aeac6114 100644 --- a/definitions/detect_variants_wgs.wdl +++ b/definitions/detect_variants_wgs.wdl @@ -34,11 +34,12 @@ workflow detectVariantsWgs { Int? readcount_minimum_base_quality Int? readcount_minimum_mapping_quality Int scatter_count - Int varscan_strand_filter = 0 - Int varscan_min_coverage = 8 - Float varscan_min_var_freq = 0.1 - Float varscan_p_value = 0.99 + Int varscan_strand_filter + Int varscan_min_coverage + Float varscan_min_var_freq + Float varscan_p_value Float? varscan_max_normal_freq + Float fp_min_var_freq File docm_vcf File docm_vcf_tbi Boolean filter_docm_variants = true @@ -80,7 +81,8 @@ workflow detectVariantsWgs { normal_bam_bai=normal_bam_bai, interval_list=roi_intervals, scatter_count=scatter_count, - tumor_sample_name=tumor_sample_name + tumor_sample_name=tumor_sample_name, + fp_min_var_freq=fp_min_var_freq } call sapp.strelkaAndPostProcessing as strelka { @@ -101,7 +103,8 @@ workflow detectVariantsWgs { exome_mode=strelka_exome_mode, cpu_reserved=strelka_cpu_reserved, call_regions=strelka_call_regions, - call_regions_tbi=strelka_call_regions_tbi + call_regions_tbi=strelka_call_regions_tbi, + fp_min_var_freq=fp_min_var_freq } call vpapp.varscanPreAndPostProcessing as varscan { @@ -122,9 +125,10 @@ workflow detectVariantsWgs { scatter_count=scatter_count, strand_filter=varscan_strand_filter, min_coverage=varscan_min_coverage, - min_var_freq=varscan_min_var_freq, + varscan_min_var_freq=varscan_min_var_freq, p_value=varscan_p_value, - max_normal_freq=varscan_max_normal_freq + max_normal_freq=varscan_max_normal_freq, + fp_min_var_freq=fp_min_var_freq } call dc.docmCle as docm { diff --git a/definitions/immuno.wdl b/definitions/immuno.wdl index 37d3d098..b63fc3ba 100644 --- a/definitions/immuno.wdl +++ b/definitions/immuno.wdl @@ -156,12 +156,14 @@ workflow immuno { Int strelka_cpu_reserved = 8 Int scatter_count = 50 - Int varscan_strand_filter = 0 - Int varscan_min_coverage = 8 - Float varscan_min_var_freq = 0.05 - Float varscan_p_value = 0.99 + Int varscan_strand_filter + Int varscan_min_coverage + Float varscan_min_var_freq + Float varscan_p_value Float? varscan_max_normal_freq + Float fp_min_var_freq + File docm_vcf File docm_vcf_tbi @@ -332,6 +334,7 @@ workflow immuno { varscan_min_var_freq=varscan_min_var_freq, varscan_p_value=varscan_p_value, varscan_max_normal_freq=varscan_max_normal_freq, + fp_min_var_freq=fp_min_var_freq, docm_vcf=docm_vcf, docm_vcf_tbi=docm_vcf_tbi, filter_docm_variants=filter_docm_variants, diff --git a/definitions/somatic_exome.wdl b/definitions/somatic_exome.wdl index 2d703909..0cb8404b 100644 --- a/definitions/somatic_exome.wdl +++ b/definitions/somatic_exome.wdl @@ -56,12 +56,14 @@ workflow somaticExome { Int strelka_cpu_reserved = 8 Int scatter_count = 50 - Int varscan_strand_filter = 0 - Int varscan_min_coverage = 8 - Float varscan_min_var_freq = 0.05 - Float varscan_p_value = 0.99 + Int varscan_strand_filter + Int varscan_min_coverage + Float varscan_min_var_freq + Float varscan_p_value Float? varscan_max_normal_freq + Float fp_min_var_freq + File docm_vcf File docm_vcf_tbi @@ -208,6 +210,7 @@ workflow somaticExome { varscan_min_var_freq=varscan_min_var_freq, varscan_p_value=varscan_p_value, varscan_max_normal_freq=varscan_max_normal_freq, + fp_min_var_freq=fp_min_var_freq, docm_vcf=docm_vcf, docm_vcf_tbi=docm_vcf_tbi, gnomad_field_name=gnomad_field_name, diff --git a/definitions/somatic_exome_cle.wdl b/definitions/somatic_exome_cle.wdl index 93a0467a..6f51bfcf 100644 --- a/definitions/somatic_exome_cle.wdl +++ b/definitions/somatic_exome_cle.wdl @@ -46,11 +46,12 @@ workflow somaticExomeCle { Int qc_minimum_base_quality = 0 Int strelka_cpu_reserved = 8 Int scatter_count - Int varscan_strand_filter = 0 - Int varscan_min_coverage = 8 - Float varscan_min_var_freq = 0.05 - Float varscan_p_value = 0.99 + Int varscan_strand_filter + Int varscan_min_coverage + Float varscan_min_var_freq + Float varscan_p_value Float? varscan_max_normal_freq + Float fp_min_var_freq File docm_vcf File docm_vcf_tbi String? gnomad_field_name @@ -169,6 +170,7 @@ workflow somaticExomeCle { varscan_min_var_freq=varscan_min_var_freq, varscan_p_value=varscan_p_value, varscan_max_normal_freq=varscan_max_normal_freq, + fp_min_var_freq=fp_min_var_freq, docm_vcf=docm_vcf, docm_vcf_tbi=docm_vcf_tbi, gnomad_field_name=gnomad_field_name, diff --git a/definitions/somatic_exome_nonhuman.wdl b/definitions/somatic_exome_nonhuman.wdl index 07759e8b..dcfc0e6d 100644 --- a/definitions/somatic_exome_nonhuman.wdl +++ b/definitions/somatic_exome_nonhuman.wdl @@ -43,12 +43,14 @@ workflow somaticExomeNonhuman { Int strelka_cpu_reserved = 8 Int scatter_count = 50 - Int varscan_strand_filter = 0 - Int varscan_min_coverage = 8 - Float varscan_min_var_freq = 0.1 - Float varscan_p_value = 0.99 + Int varscan_strand_filter + Int varscan_min_coverage + Float varscan_min_var_freq + Float varscan_p_value Float? varscan_max_normal_freq + Float fp_min_var_freq + File vep_cache_dir_zip String vep_ensembl_assembly String vep_ensembl_version @@ -142,6 +144,7 @@ workflow somaticExomeNonhuman { varscan_min_var_freq=varscan_min_var_freq, varscan_p_value=varscan_p_value, varscan_max_normal_freq=varscan_max_normal_freq, + fp_min_var_freq=fp_min_var_freq, filter_somatic_llr_threshold=filter_somatic_llr_threshold, filter_somatic_llr_tumor_purity=filter_somatic_llr_tumor_purity, filter_somatic_llr_normal_contamination_rate=filter_somatic_llr_normal_contamination_rate, diff --git a/definitions/somatic_wgs.wdl b/definitions/somatic_wgs.wdl index acc38833..9886065a 100644 --- a/definitions/somatic_wgs.wdl +++ b/definitions/somatic_wgs.wdl @@ -51,16 +51,16 @@ workflow somaticWgs { File? strelka_call_regions File? strelka_call_regions_tbi Int scatter_count - Int varscan_strand_filter = 0 - Int varscan_min_coverage = 8 - Float varscan_min_var_freq = 0.05 - Float varscan_p_value = 0.99 + Int varscan_strand_filter + Int varscan_min_coverage + Float varscan_min_var_freq + Float varscan_p_value Float? varscan_max_normal_freq + Float fp_min_var_freq File docm_vcf File docm_vcf_tbi Boolean filter_docm_variants = true - Float filter_somatic_llr_threshold = 5 Float filter_somatic_llr_tumor_purity = 1 Float filter_somatic_llr_normal_contamination_rate = 0 @@ -192,6 +192,7 @@ workflow somaticWgs { varscan_min_var_freq=varscan_min_var_freq, varscan_p_value=varscan_p_value, varscan_max_normal_freq=varscan_max_normal_freq, + fp_min_var_freq=fp_min_var_freq, docm_vcf=docm_vcf, docm_vcf_tbi=docm_vcf_tbi, filter_docm_variants=filter_docm_variants, diff --git a/definitions/subworkflows/fp_filter.wdl b/definitions/subworkflows/fp_filter.wdl index 7f886ba5..2f6aa0ae 100644 --- a/definitions/subworkflows/fp_filter.wdl +++ b/definitions/subworkflows/fp_filter.wdl @@ -19,7 +19,7 @@ workflow fpFilter { File vcf_tbi String variant_caller String? sample_name - Float? min_var_freq + Float? fp_min_var_freq } call vs.vcfSanitize as sanitizeVcf { @@ -53,7 +53,7 @@ workflow fpFilter { bam=bam, vcf=index.indexed_vcf, sample_name=sample_name, - min_var_freq=min_var_freq, + fp_min_var_freq=fp_min_var_freq, output_vcf_basename = variant_caller + "_full" } diff --git a/definitions/subworkflows/mutect.wdl b/definitions/subworkflows/mutect.wdl index 56fd24b9..dc22e8c4 100644 --- a/definitions/subworkflows/mutect.wdl +++ b/definitions/subworkflows/mutect.wdl @@ -22,6 +22,7 @@ workflow mutect { File interval_list Int scatter_count String tumor_sample_name + Float fp_min_var_freq } call sil.splitIntervalList { @@ -64,7 +65,8 @@ workflow mutect { vcf=indexVcf.indexed_vcf, vcf_tbi=indexVcf.indexed_vcf_tbi, variant_caller="mutect", - sample_name=tumor_sample_name + sample_name=tumor_sample_name, + fp_min_var_freq=fp_min_var_freq } output { diff --git a/definitions/subworkflows/pindel.wdl b/definitions/subworkflows/pindel.wdl index ae9947ee..34f83567 100644 --- a/definitions/subworkflows/pindel.wdl +++ b/definitions/subworkflows/pindel.wdl @@ -23,6 +23,7 @@ workflow pindel { String normal_sample_name Int insert_size = 400 Int scatter_count = 50 + Float fp_min_var_freq } call siltb.splitIntervalListToBed { @@ -88,7 +89,8 @@ workflow pindel { vcf=reindex.indexed_vcf, vcf_tbi=reindex.indexed_vcf_tbi, variant_caller="pindel", - sample_name=tumor_sample_name + sample_name=tumor_sample_name, + fp_min_var_freq=fp_min_var_freq } output { diff --git a/definitions/subworkflows/strelka_and_post_processing.wdl b/definitions/subworkflows/strelka_and_post_processing.wdl index 3ac04378..ef27aa42 100644 --- a/definitions/subworkflows/strelka_and_post_processing.wdl +++ b/definitions/subworkflows/strelka_and_post_processing.wdl @@ -29,6 +29,8 @@ workflow strelkaAndPostProcessing { File? call_regions File? call_regions_tbi + + Float fp_min_var_freq } call s.strelka { @@ -96,7 +98,8 @@ workflow strelkaAndPostProcessing { vcf=regionFilter.filtered_vcf, vcf_tbi=regionFilter.filtered_vcf_tbi, sample_name=tumor_sample_name, - variant_caller="strelka" + variant_caller="strelka", + fp_min_var_freq=fp_min_var_freq } output { diff --git a/definitions/subworkflows/varscan.wdl b/definitions/subworkflows/varscan.wdl index e480672d..7844e1e9 100644 --- a/definitions/subworkflows/varscan.wdl +++ b/definitions/subworkflows/varscan.wdl @@ -17,10 +17,10 @@ workflow varscan { File? roi_bed - Int strand_filter = 0 - Int min_coverage = 8 - Float min_var_freq = 0.1 - Float p_value = 0.99 + Int strand_filter + Int min_coverage + Float varscan_min_var_freq + Float p_value Float? max_normal_freq } @@ -36,7 +36,7 @@ workflow varscan { roi_bed=roi_bed, strand_filter=strand_filter, min_coverage=min_coverage, - min_var_freq=min_var_freq, + varscan_min_var_freq=varscan_min_var_freq, p_value=p_value } @@ -52,7 +52,6 @@ workflow varscan { max_normal_freq=max_normal_freq } - output { # somatic File snvs = somatic.snvs diff --git a/definitions/subworkflows/varscan_pre_and_post_processing.wdl b/definitions/subworkflows/varscan_pre_and_post_processing.wdl index 350d4c1a..317460bd 100644 --- a/definitions/subworkflows/varscan_pre_and_post_processing.wdl +++ b/definitions/subworkflows/varscan_pre_and_post_processing.wdl @@ -26,10 +26,11 @@ workflow varscanPreAndPostProcessing { File interval_list - Int strand_filter = 0 - Int min_coverage = 8 - Float min_var_freq = 0.1 - Float p_value = 0.99 + Int strand_filter + Int min_coverage + Float varscan_min_var_freq + Float fp_min_var_freq + Float p_value Float? max_normal_freq Int scatter_count = 50 } @@ -57,7 +58,7 @@ workflow varscanPreAndPostProcessing { roi_bed=intervalsToBed.interval_bed, strand_filter=strand_filter, min_coverage=min_coverage, - min_var_freq=min_var_freq, + varscan_min_var_freq=varscan_min_var_freq, p_value=p_value, max_normal_freq=max_normal_freq } @@ -154,7 +155,7 @@ workflow varscanPreAndPostProcessing { bam_bai=tumor_bam_bai, vcf=index.indexed_vcf, vcf_tbi=index.indexed_vcf_tbi, - min_var_freq=min_var_freq, + fp_min_var_freq=fp_min_var_freq, sample_name=tumor_sample_name, variant_caller="varscan" } diff --git a/definitions/tools/fp_filter.wdl b/definitions/tools/fp_filter.wdl index 9d151123..a5c33956 100644 --- a/definitions/tools/fp_filter.wdl +++ b/definitions/tools/fp_filter.wdl @@ -11,7 +11,7 @@ task fpFilter { String output_vcf_basename = "fpfilter" String sample_name = "TUMOR" - Float min_var_freq = 0.05 + Float fp_min_var_freq = 0.05 } Int space_needed_gb = 10 + round(size(vcf, "GB")*2 + size([reference, reference_fai, reference_dict, bam], "GB")) @@ -26,7 +26,7 @@ task fpFilter { String output_vcf = output_vcf_basename + ".vcf" command <<< - /usr/bin/perl /usr/bin/fpfilter.pl --bam-readcount /usr/bin/bam-readcount --samtools /opt/samtools/bin/samtools --output ~{output_vcf} --reference ~{reference} --bam-file ~{bam} --vcf-file ~{vcf} --sample ~{sample_name} --min-var-freq ~{min_var_freq} + /usr/bin/perl /usr/bin/fpfilter.pl --bam-readcount /usr/bin/bam-readcount --samtools /opt/samtools/bin/samtools --output ~{output_vcf} --reference ~{reference} --bam-file ~{bam} --vcf-file ~{vcf} --sample ~{sample_name} --min-var-freq ~{fp_min_var_freq} >>> output { diff --git a/definitions/tools/varscan_somatic.wdl b/definitions/tools/varscan_somatic.wdl index 9bf0eced..a8eb7763 100644 --- a/definitions/tools/varscan_somatic.wdl +++ b/definitions/tools/varscan_somatic.wdl @@ -72,10 +72,10 @@ workflow wf { File normal_bam File normal_bam_bai - Int strand_filter = 0 - Int min_coverage = 8 - Float min_var_freq = 0.1 - Float p_value = 0.99 + Int strand_filter + Int min_coverage + Float min_var_freq + Float p_value File? roi_bed } diff --git a/definitions/tumor_only_detect_variants.wdl b/definitions/tumor_only_detect_variants.wdl index 71f0ecf1..e1c23cf0 100644 --- a/definitions/tumor_only_detect_variants.wdl +++ b/definitions/tumor_only_detect_variants.wdl @@ -31,11 +31,11 @@ workflow tumorOnlyDetectVariants { String gnomad_field_name = "gnomADe_AF" # only change with gnomad_filter_annotation File roi_intervals - Int varscan_strand_filter = 0 - Int varscan_min_coverage = 8 - Int varscan_min_reads = 2 - Float varscan_min_var_freq = 0.1 - Float varscan_p_value = 0.99 + Int varscan_strand_filter + Int varscan_min_coverage + Int varscan_min_reads + Float varscan_min_var_freq + Float varscan_p_value Float maximum_population_allele_frequency = 0.001 File vep_cache_dir_zip diff --git a/definitions/tumor_only_exome.wdl b/definitions/tumor_only_exome.wdl index 74713736..857192b4 100644 --- a/definitions/tumor_only_exome.wdl +++ b/definitions/tumor_only_exome.wdl @@ -34,11 +34,11 @@ workflow tumorOnlyExome { File omni_vcf_tbi String picard_metric_accumulation_level Int target_interval_padding = 100 - Int varscan_strand_filter = 0 - Int varscan_min_coverage = 8 - Float varscan_min_var_freq = 0.1 - Float varscan_p_value = 0.99 - Int varscan_min_reads = 2 + Int varscan_strand_filter + Int varscan_min_coverage + Float varscan_min_var_freq + Float varscan_p_value + Int varscan_min_reads Float maximum_population_allele_frequency = 0.001 File vep_cache_dir_zip diff --git a/definitions/tumor_only_wgs.wdl b/definitions/tumor_only_wgs.wdl index fb3383c8..f6a75f2e 100644 --- a/definitions/tumor_only_wgs.wdl +++ b/definitions/tumor_only_wgs.wdl @@ -58,9 +58,9 @@ workflow tumorOnlyWgs { Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF"] Array[String] variants_to_table_genotype_fields = ["GT", "AD"] Array[String] vep_to_table_fields = ["HGVSc", "HGVSp"] - Int varscan_min_coverage = 8 - Float varscan_min_var_freq = 0.05 - Int varscan_min_reads = 2 + Int varscan_min_coverage + Float varscan_min_var_freq + Int varscan_min_reads Float maximum_population_allele_frequency = 0.001 } From d37fa0d97bd84f965235ad49504ceef7e960201b Mon Sep 17 00:00:00 2001 From: Malachi Griffith Date: Tue, 11 Apr 2023 16:00:36 -0500 Subject: [PATCH 02/10] make use of var frequency variables more consistent --- definitions/tools/varscan_somatic.wdl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/definitions/tools/varscan_somatic.wdl b/definitions/tools/varscan_somatic.wdl index a8eb7763..d61a2f22 100644 --- a/definitions/tools/varscan_somatic.wdl +++ b/definitions/tools/varscan_somatic.wdl @@ -14,7 +14,7 @@ task varscanSomatic { Int strand_filter = 0 Int min_coverage = 8 - Float min_var_freq = 0.1 + Float varscan_min_var_freq = 0.1 Float p_value = 0.99 File? roi_bed } @@ -48,7 +48,7 @@ task varscanSomatic { "output" \ --strand-filter "~{strand_filter}" \ --min-coverage "~{min_coverage}" \ - --min-var-freq "~{min_var_freq}" \ + --min-var-freq "~{varscan_min_var_freq}" \ --p-value "~{p_value}" \ --mpileup 1 \ --output-vcf @@ -74,7 +74,7 @@ workflow wf { Int strand_filter Int min_coverage - Float min_var_freq + Float varscan_min_var_freq Float p_value File? roi_bed } @@ -90,7 +90,7 @@ workflow wf { normal_bam_bai=normal_bam_bai, strand_filter=strand_filter, min_coverage=min_coverage, - min_var_freq=min_var_freq, + varscan_min_var_freq=varscan_min_var_freq, p_value=p_value, roi_bed=roi_bed } From 3a18642223a5960ee284106e920f769822962b07 Mon Sep 17 00:00:00 2001 From: Malachi Griffith Date: Tue, 11 Apr 2023 16:59:39 -0500 Subject: [PATCH 03/10] fix min var freq variables for tumor only variant calling wdls --- definitions/subworkflows/varscan_germline.wdl | 15 ++++++++------- definitions/tools/varscan_germline.wdl | 4 ++-- definitions/tumor_only_detect_variants.wdl | 5 ++++- definitions/tumor_only_exome.wdl | 2 ++ definitions/tumor_only_wgs.wdl | 2 ++ 5 files changed, 18 insertions(+), 10 deletions(-) diff --git a/definitions/subworkflows/varscan_germline.wdl b/definitions/subworkflows/varscan_germline.wdl index 7d1dfa29..e5c73c5d 100644 --- a/definitions/subworkflows/varscan_germline.wdl +++ b/definitions/subworkflows/varscan_germline.wdl @@ -13,11 +13,12 @@ workflow varscanGermline { File reference_fai File reference_dict File interval_list - Int strand_filter = 0 - Int min_coverage = 8 - Float min_var_freq = 0.1 - Int min_reads = 2 - Float p_value = 0.99 + Int strand_filter + Int min_coverage + Float varscan_min_var_freq + Int min_reads + Float p_value + Fooat fp_min_var_freq String sample_name } @@ -36,7 +37,7 @@ workflow varscanGermline { roi_bed=intervalsToBed.interval_bed, strand_filter=strand_filter, min_coverage=min_coverage, - min_var_freq=min_var_freq, + varscan_min_var_freq=varscan_min_var_freq, min_reads=min_reads, p_value=p_value, sample_name=sample_name @@ -58,7 +59,7 @@ workflow varscanGermline { vcf_tbi=bgzipAndIndex.indexed_vcf_tbi, variant_caller="varscan", sample_name=sample_name, - min_var_freq=min_var_freq + fp_min_var_freq=fp_min_var_freq } output { diff --git a/definitions/tools/varscan_germline.wdl b/definitions/tools/varscan_germline.wdl index 8103a25f..53a1af6e 100644 --- a/definitions/tools/varscan_germline.wdl +++ b/definitions/tools/varscan_germline.wdl @@ -9,7 +9,7 @@ task varscanGermline { File reference_dict Int strand_filter = 0 Int min_coverage = 8 - Float min_var_freq = 0.1 + Float varscan_min_var_freq = 0.1 Int min_reads = 2 Float p_value = 0.99 String sample_name @@ -33,7 +33,7 @@ task varscanGermline { ~{reference} \ ~{strand_filter} \ ~{min_coverage} \ - ~{min_var_freq} \ + ~{varscan_min_var_freq} \ ~{min_reads} \ ~{p_value} \ ~{sample_name} \ diff --git a/definitions/tumor_only_detect_variants.wdl b/definitions/tumor_only_detect_variants.wdl index e1c23cf0..c1be0f5c 100644 --- a/definitions/tumor_only_detect_variants.wdl +++ b/definitions/tumor_only_detect_variants.wdl @@ -38,6 +38,8 @@ workflow tumorOnlyDetectVariants { Float varscan_p_value Float maximum_population_allele_frequency = 0.001 + Float fp_min_var_freq + File vep_cache_dir_zip String vep_ensembl_assembly String vep_ensembl_version @@ -71,9 +73,10 @@ workflow tumorOnlyDetectVariants { interval_list=roi_intervals, strand_filter=varscan_strand_filter, min_coverage=varscan_min_coverage, - min_var_freq=varscan_min_var_freq, + varscan_min_var_freq=varscan_min_var_freq, min_reads=varscan_min_reads, p_value=varscan_p_value, + fp_min_var_freq=fp_min_var_freq, sample_name=sample_name } diff --git a/definitions/tumor_only_exome.wdl b/definitions/tumor_only_exome.wdl index 857192b4..b2649823 100644 --- a/definitions/tumor_only_exome.wdl +++ b/definitions/tumor_only_exome.wdl @@ -39,6 +39,7 @@ workflow tumorOnlyExome { Float varscan_min_var_freq Float varscan_p_value Int varscan_min_reads + Float fp_min_var_freq Float maximum_population_allele_frequency = 0.001 File vep_cache_dir_zip @@ -107,6 +108,7 @@ workflow tumorOnlyExome { varscan_min_var_freq=varscan_min_var_freq, varscan_p_value=varscan_p_value, varscan_min_reads=varscan_min_reads, + fp_min_var_freq=fp_min_var_freq, maximum_population_allele_frequency=maximum_population_allele_frequency, vep_cache_dir_zip=vep_cache_dir_zip, vep_ensembl_assembly=vep_ensembl_assembly, diff --git a/definitions/tumor_only_wgs.wdl b/definitions/tumor_only_wgs.wdl index f6a75f2e..bafabf52 100644 --- a/definitions/tumor_only_wgs.wdl +++ b/definitions/tumor_only_wgs.wdl @@ -61,6 +61,7 @@ workflow tumorOnlyWgs { Int varscan_min_coverage Float varscan_min_var_freq Int varscan_min_reads + Float fp_min_var_freq Float maximum_population_allele_frequency = 0.001 } @@ -102,6 +103,7 @@ workflow tumorOnlyWgs { varscan_min_coverage=varscan_min_coverage, varscan_min_var_freq=varscan_min_var_freq, varscan_min_reads=varscan_min_reads, + fp_min_var_freq=fp_min_var_freq, maximum_population_allele_frequency=maximum_population_allele_frequency, vep_cache_dir_zip=vep_cache_dir_zip, synonyms_file=synonyms_file, From e06cac393c8313d98475b715526bd40082b600ba Mon Sep 17 00:00:00 2001 From: Malachi Griffith Date: Thu, 13 Apr 2023 11:34:08 -0500 Subject: [PATCH 04/10] the cutoff used for varscan tool and fp_filter of varscan results should be the same --- definitions/detect_variants.wdl | 1 - definitions/detect_variants_nonhuman.wdl | 1 - definitions/detect_variants_wgs.wdl | 3 +-- definitions/subworkflows/varscan_germline.wdl | 3 +-- definitions/subworkflows/varscan_pre_and_post_processing.wdl | 3 +-- definitions/tools/varscan_germline.wdl | 2 +- definitions/tools/varscan_somatic.wdl | 2 +- definitions/tumor_only_detect_variants.wdl | 3 --- 8 files changed, 5 insertions(+), 13 deletions(-) diff --git a/definitions/detect_variants.wdl b/definitions/detect_variants.wdl index 591bcf2f..53306c9b 100644 --- a/definitions/detect_variants.wdl +++ b/definitions/detect_variants.wdl @@ -128,7 +128,6 @@ workflow detectVariants { varscan_min_var_freq=varscan_min_var_freq, p_value=varscan_p_value, max_normal_freq=varscan_max_normal_freq, - fp_min_var_freq=fp_min_var_freq, normal_sample_name=normal_sample_name, tumor_sample_name=tumor_sample_name } diff --git a/definitions/detect_variants_nonhuman.wdl b/definitions/detect_variants_nonhuman.wdl index 5b79d780..6bd5bfec 100644 --- a/definitions/detect_variants_nonhuman.wdl +++ b/definitions/detect_variants_nonhuman.wdl @@ -113,7 +113,6 @@ workflow detectVariantsNonhuman { varscan_min_var_freq=varscan_min_var_freq, p_value=varscan_p_value, max_normal_freq=varscan_max_normal_freq, - fp_min_var_freq=fp_min_var_freq, normal_sample_name=normal_sample_name, tumor_sample_name=tumor_sample_name } diff --git a/definitions/detect_variants_wgs.wdl b/definitions/detect_variants_wgs.wdl index aeac6114..01b3a719 100644 --- a/definitions/detect_variants_wgs.wdl +++ b/definitions/detect_variants_wgs.wdl @@ -127,8 +127,7 @@ workflow detectVariantsWgs { min_coverage=varscan_min_coverage, varscan_min_var_freq=varscan_min_var_freq, p_value=varscan_p_value, - max_normal_freq=varscan_max_normal_freq, - fp_min_var_freq=fp_min_var_freq + max_normal_freq=varscan_max_normal_freq } call dc.docmCle as docm { diff --git a/definitions/subworkflows/varscan_germline.wdl b/definitions/subworkflows/varscan_germline.wdl index e5c73c5d..19e78c43 100644 --- a/definitions/subworkflows/varscan_germline.wdl +++ b/definitions/subworkflows/varscan_germline.wdl @@ -18,7 +18,6 @@ workflow varscanGermline { Float varscan_min_var_freq Int min_reads Float p_value - Fooat fp_min_var_freq String sample_name } @@ -59,7 +58,7 @@ workflow varscanGermline { vcf_tbi=bgzipAndIndex.indexed_vcf_tbi, variant_caller="varscan", sample_name=sample_name, - fp_min_var_freq=fp_min_var_freq + fp_min_var_freq=varscan_min_var_freq } output { diff --git a/definitions/subworkflows/varscan_pre_and_post_processing.wdl b/definitions/subworkflows/varscan_pre_and_post_processing.wdl index 317460bd..c3038891 100644 --- a/definitions/subworkflows/varscan_pre_and_post_processing.wdl +++ b/definitions/subworkflows/varscan_pre_and_post_processing.wdl @@ -29,7 +29,6 @@ workflow varscanPreAndPostProcessing { Int strand_filter Int min_coverage Float varscan_min_var_freq - Float fp_min_var_freq Float p_value Float? max_normal_freq Int scatter_count = 50 @@ -155,7 +154,7 @@ workflow varscanPreAndPostProcessing { bam_bai=tumor_bam_bai, vcf=index.indexed_vcf, vcf_tbi=index.indexed_vcf_tbi, - fp_min_var_freq=fp_min_var_freq, + fp_min_var_freq=varscan_min_var_freq, sample_name=tumor_sample_name, variant_caller="varscan" } diff --git a/definitions/tools/varscan_germline.wdl b/definitions/tools/varscan_germline.wdl index 53a1af6e..92189709 100644 --- a/definitions/tools/varscan_germline.wdl +++ b/definitions/tools/varscan_germline.wdl @@ -9,7 +9,7 @@ task varscanGermline { File reference_dict Int strand_filter = 0 Int min_coverage = 8 - Float varscan_min_var_freq = 0.1 + Float varscan_min_var_freq = 0.05 Int min_reads = 2 Float p_value = 0.99 String sample_name diff --git a/definitions/tools/varscan_somatic.wdl b/definitions/tools/varscan_somatic.wdl index d61a2f22..2344e618 100644 --- a/definitions/tools/varscan_somatic.wdl +++ b/definitions/tools/varscan_somatic.wdl @@ -14,7 +14,7 @@ task varscanSomatic { Int strand_filter = 0 Int min_coverage = 8 - Float varscan_min_var_freq = 0.1 + Float varscan_min_var_freq = 0.05 Float p_value = 0.99 File? roi_bed } diff --git a/definitions/tumor_only_detect_variants.wdl b/definitions/tumor_only_detect_variants.wdl index c1be0f5c..f53c833e 100644 --- a/definitions/tumor_only_detect_variants.wdl +++ b/definitions/tumor_only_detect_variants.wdl @@ -38,8 +38,6 @@ workflow tumorOnlyDetectVariants { Float varscan_p_value Float maximum_population_allele_frequency = 0.001 - Float fp_min_var_freq - File vep_cache_dir_zip String vep_ensembl_assembly String vep_ensembl_version @@ -76,7 +74,6 @@ workflow tumorOnlyDetectVariants { varscan_min_var_freq=varscan_min_var_freq, min_reads=varscan_min_reads, p_value=varscan_p_value, - fp_min_var_freq=fp_min_var_freq, sample_name=sample_name } From 24aed9bb80bf0ef31adc2d1ec0d469a7e4b5937d Mon Sep 17 00:00:00 2001 From: Malachi Griffith Date: Thu, 13 Apr 2023 13:54:33 -0500 Subject: [PATCH 05/10] pass llr settings in from immuno and drop defaults being set everywhere --- definitions/detect_variants.wdl | 6 +++--- definitions/detect_variants_wgs.wdl | 6 +++--- definitions/immuno.wdl | 8 ++++++++ definitions/somatic_exome.wdl | 6 +++--- definitions/somatic_exome_cle.wdl | 6 +++--- definitions/somatic_exome_nonhuman.wdl | 6 +++--- definitions/somatic_wgs.wdl | 6 +++--- definitions/tools/filter_vcf_somatic_llr.wdl | 2 +- 8 files changed, 27 insertions(+), 19 deletions(-) diff --git a/definitions/detect_variants.wdl b/definitions/detect_variants.wdl index 53306c9b..7dd6417e 100644 --- a/definitions/detect_variants.wdl +++ b/definitions/detect_variants.wdl @@ -67,9 +67,9 @@ workflow detectVariants { Float filter_gnomADe_maximum_population_allele_frequency = 0.001 Float filter_mapq0_threshold = 0.15 - Float filter_somatic_llr_threshold = 5 - Float filter_somatic_llr_tumor_purity = 1 - Float filter_somatic_llr_normal_contamination_rate = 0 + Float filter_somatic_llr_threshold + Float filter_somatic_llr_tumor_purity + Float filter_somatic_llr_normal_contamination_rate Int filter_minimum_depth = 1 Boolean cle_vcf_filter = false Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF"] diff --git a/definitions/detect_variants_wgs.wdl b/definitions/detect_variants_wgs.wdl index 01b3a719..9a6724cc 100644 --- a/definitions/detect_variants_wgs.wdl +++ b/definitions/detect_variants_wgs.wdl @@ -56,9 +56,9 @@ workflow detectVariantsWgs { Float filter_gnomADe_maximum_population_allele_frequency = 0.001 Float filter_mapq0_threshold = 0.15 Int filter_minimum_depth = 1 - Float filter_somatic_llr_threshold = 5 - Float filter_somatic_llr_tumor_purity = 1 - Float filter_somatic_llr_normal_contamination_rate = 0 + Float filter_somatic_llr_threshold + Float filter_somatic_llr_tumor_purity + Float filter_somatic_llr_normal_contamination_rate Boolean cle_vcf_filter = false Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF"] Array[String] variants_to_table_genotype_fields = ["GT", "AD"] diff --git a/definitions/immuno.wdl b/definitions/immuno.wdl index b63fc3ba..16026c3e 100644 --- a/definitions/immuno.wdl +++ b/definitions/immuno.wdl @@ -181,6 +181,11 @@ workflow immuno { # one of [pick, flag_pick, pick-allele, per_gene, pick_allele_gene, flag_pick_allele, flag_pick_allele_gene] String? vep_pick Boolean cle_vcf_filter = false + + Float filter_somatic_llr_threshold + Float filter_somatic_llr_tumor_purity + Float filter_somatic_llr_normal_contamination_rate + Array[String] vep_to_table_fields = ["HGVSc", "HGVSp"] Array[String] variants_to_table_genotype_fields = ["GT", "AD"] Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF"] @@ -346,6 +351,9 @@ workflow immuno { annotate_coding_only=annotate_coding_only, vep_pick=vep_pick, cle_vcf_filter=cle_vcf_filter, + filter_somatic_llr_threshold=filter_somatic_llr_threshold, + filter_somatic_llr_tumor_purity=filter_somatic_llr_tumor_purity, + filter_somatic_llr_normal_contamination_rate=filter_somatic_llr_normal_contamination_rate, variants_to_table_fields=variants_to_table_fields, variants_to_table_genotype_fields=variants_to_table_genotype_fields, vep_to_table_fields=vep_to_table_fields, diff --git a/definitions/somatic_exome.wdl b/definitions/somatic_exome.wdl index 0cb8404b..144c8bd5 100644 --- a/definitions/somatic_exome.wdl +++ b/definitions/somatic_exome.wdl @@ -72,9 +72,9 @@ workflow somaticExome { String? gnomad_field_name Float? filter_gnomADe_maximum_population_allele_frequency - Float filter_somatic_llr_threshold = 5 - Float filter_somatic_llr_tumor_purity = 1 - Float filter_somatic_llr_normal_contamination_rate = 0 + Float filter_somatic_llr_threshold + Float filter_somatic_llr_tumor_purity + Float filter_somatic_llr_normal_contamination_rate File vep_cache_dir_zip String vep_ensembl_assembly diff --git a/definitions/somatic_exome_cle.wdl b/definitions/somatic_exome_cle.wdl index 6f51bfcf..2ea8577d 100644 --- a/definitions/somatic_exome_cle.wdl +++ b/definitions/somatic_exome_cle.wdl @@ -58,9 +58,9 @@ workflow somaticExomeCle { Float? filter_gnomADe_maximum_population_allele_frequency Boolean filter_docm_variants = true Int filter_minimum_depth = 20 - Float filter_somatic_llr_threshold = 5 - Float filter_somatic_llr_tumor_purity = 1.0 - Float filter_somatic_llr_normal_contamination_rate = 0.0 + Float filter_somatic_llr_threshold + Float filter_somatic_llr_tumor_purity + Float filter_somatic_llr_normal_contamination_rate File vep_cache_dir_zip String vep_ensembl_assembly String vep_ensembl_version diff --git a/definitions/somatic_exome_nonhuman.wdl b/definitions/somatic_exome_nonhuman.wdl index dcfc0e6d..6b4f2bdf 100644 --- a/definitions/somatic_exome_nonhuman.wdl +++ b/definitions/somatic_exome_nonhuman.wdl @@ -61,9 +61,9 @@ workflow somaticExomeNonhuman { String? vep_pick Boolean cle_vcf_filter = false - Float filter_somatic_llr_threshold = 5 - Float filter_somatic_llr_tumor_purity = 1 - Float filter_somatic_llr_normal_contamination_rate = 0 + Float filter_somatic_llr_threshold + Float filter_somatic_llr_tumor_purity + Float filter_somatic_llr_normal_contamination_rate Array[String] vep_to_table_fields = ["Consequence", "SYMBOL", "Feature"] Array[String] variants_to_table_genotype_fields = ["GT", "AD"] diff --git a/definitions/somatic_wgs.wdl b/definitions/somatic_wgs.wdl index 9886065a..f7b64097 100644 --- a/definitions/somatic_wgs.wdl +++ b/definitions/somatic_wgs.wdl @@ -61,9 +61,9 @@ workflow somaticWgs { File docm_vcf_tbi Boolean filter_docm_variants = true - Float filter_somatic_llr_threshold = 5 - Float filter_somatic_llr_tumor_purity = 1 - Float filter_somatic_llr_normal_contamination_rate = 0 + Float filter_somatic_llr_threshold + Float filter_somatic_llr_tumor_purity + Float filter_somatic_llr_normal_contamination_rate File vep_cache_dir_zip String vep_ensembl_assembly String vep_ensembl_version diff --git a/definitions/tools/filter_vcf_somatic_llr.wdl b/definitions/tools/filter_vcf_somatic_llr.wdl index 5cc9e28a..f68e9782 100644 --- a/definitions/tools/filter_vcf_somatic_llr.wdl +++ b/definitions/tools/filter_vcf_somatic_llr.wdl @@ -3,9 +3,9 @@ version 1.0 task filterVcfSomaticLlr { input { File vcf - Float threshold String tumor_sample_name String normal_sample_name + Float threshold = 5 Float tumor_purity = 1 Float normal_contamination_rate = 0 } From 7548f31b4ab119391a0167522295bd7d3a451275 Mon Sep 17 00:00:00 2001 From: Malachi Griffith Date: Thu, 13 Apr 2023 16:49:01 -0500 Subject: [PATCH 06/10] remove incorrect input --- definitions/tumor_only_exome.wdl | 1 - 1 file changed, 1 deletion(-) diff --git a/definitions/tumor_only_exome.wdl b/definitions/tumor_only_exome.wdl index b2649823..c4d30ffc 100644 --- a/definitions/tumor_only_exome.wdl +++ b/definitions/tumor_only_exome.wdl @@ -108,7 +108,6 @@ workflow tumorOnlyExome { varscan_min_var_freq=varscan_min_var_freq, varscan_p_value=varscan_p_value, varscan_min_reads=varscan_min_reads, - fp_min_var_freq=fp_min_var_freq, maximum_population_allele_frequency=maximum_population_allele_frequency, vep_cache_dir_zip=vep_cache_dir_zip, vep_ensembl_assembly=vep_ensembl_assembly, From d312b408c5d81efa3677ad1fd07edb1f9721c8ec Mon Sep 17 00:00:00 2001 From: Malachi Griffith Date: Thu, 13 Apr 2023 21:14:29 -0500 Subject: [PATCH 07/10] remove incorrect input --- definitions/tumor_only_wgs.wdl | 2 -- 1 file changed, 2 deletions(-) diff --git a/definitions/tumor_only_wgs.wdl b/definitions/tumor_only_wgs.wdl index bafabf52..f6a75f2e 100644 --- a/definitions/tumor_only_wgs.wdl +++ b/definitions/tumor_only_wgs.wdl @@ -61,7 +61,6 @@ workflow tumorOnlyWgs { Int varscan_min_coverage Float varscan_min_var_freq Int varscan_min_reads - Float fp_min_var_freq Float maximum_population_allele_frequency = 0.001 } @@ -103,7 +102,6 @@ workflow tumorOnlyWgs { varscan_min_coverage=varscan_min_coverage, varscan_min_var_freq=varscan_min_var_freq, varscan_min_reads=varscan_min_reads, - fp_min_var_freq=fp_min_var_freq, maximum_population_allele_frequency=maximum_population_allele_frequency, vep_cache_dir_zip=vep_cache_dir_zip, synonyms_file=synonyms_file, From cf974ecf6c0e26187a35132f453ab64e558bfb86 Mon Sep 17 00:00:00 2001 From: Malachi Griffith Date: Fri, 21 Apr 2023 10:12:07 -0500 Subject: [PATCH 08/10] make parameters optional now that defaults are not being specified --- definitions/detect_variants.wdl | 16 ++++++++-------- definitions/detect_variants_nonhuman.wdl | 16 ++++++++-------- definitions/detect_variants_wgs.wdl | 16 ++++++++-------- definitions/immuno.wdl | 16 ++++++++-------- definitions/somatic_exome.wdl | 16 ++++++++-------- definitions/somatic_exome_cle.wdl | 16 ++++++++-------- definitions/somatic_exome_nonhuman.wdl | 16 ++++++++-------- definitions/somatic_wgs.wdl | 16 ++++++++-------- definitions/subworkflows/mutect.wdl | 2 +- definitions/subworkflows/pindel.wdl | 2 +- .../subworkflows/strelka_and_post_processing.wdl | 2 +- definitions/subworkflows/varscan.wdl | 8 ++++---- definitions/subworkflows/varscan_germline.wdl | 10 +++++----- .../varscan_pre_and_post_processing.wdl | 8 ++++---- definitions/tumor_only_detect_variants.wdl | 10 +++++----- definitions/tumor_only_exome.wdl | 12 ++++++------ definitions/tumor_only_wgs.wdl | 6 +++--- 17 files changed, 94 insertions(+), 94 deletions(-) diff --git a/definitions/detect_variants.wdl b/definitions/detect_variants.wdl index 7dd6417e..25e75d2e 100644 --- a/definitions/detect_variants.wdl +++ b/definitions/detect_variants.wdl @@ -36,13 +36,13 @@ workflow detectVariants { Boolean strelka_exome_mode Int strelka_cpu_reserved = 8 - Int varscan_strand_filter - Int varscan_min_coverage - Float varscan_min_var_freq - Float varscan_p_value + Int? varscan_strand_filter + Int? varscan_min_coverage + Float? varscan_min_var_freq + Float? varscan_p_value Float? varscan_max_normal_freq - Float fp_min_var_freq + Float? fp_min_var_freq File docm_vcf File docm_vcf_tbi @@ -67,9 +67,9 @@ workflow detectVariants { Float filter_gnomADe_maximum_population_allele_frequency = 0.001 Float filter_mapq0_threshold = 0.15 - Float filter_somatic_llr_threshold - Float filter_somatic_llr_tumor_purity - Float filter_somatic_llr_normal_contamination_rate + Float? filter_somatic_llr_threshold + Float? filter_somatic_llr_tumor_purity + Float? filter_somatic_llr_normal_contamination_rate Int filter_minimum_depth = 1 Boolean cle_vcf_filter = false Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF"] diff --git a/definitions/detect_variants_nonhuman.wdl b/definitions/detect_variants_nonhuman.wdl index 6bd5bfec..f934f8f9 100644 --- a/definitions/detect_variants_nonhuman.wdl +++ b/definitions/detect_variants_nonhuman.wdl @@ -33,13 +33,13 @@ workflow detectVariantsNonhuman { Boolean strelka_exome_mode Int strelka_cpu_reserved = 8 - Int varscan_strand_filter - Int varscan_min_coverage - Float varscan_min_var_freq - Float varscan_p_value + Int? varscan_strand_filter + Int? varscan_min_coverage + Float? varscan_min_var_freq + Float? varscan_p_value Float? varscan_max_normal_freq - Float fp_min_var_freq + Float? fp_min_var_freq File vep_cache_dir_zip String vep_ensembl_assembly @@ -55,9 +55,9 @@ workflow detectVariantsNonhuman { Int? readcount_minimum_mapping_quality Float filter_mapq0_threshold = 0.15 - Float filter_somatic_llr_threshold = 5 - Float filter_somatic_llr_tumor_purity = 1 - Float filter_somatic_llr_normal_contamination_rate = 0 + Float? filter_somatic_llr_threshold + Float? filter_somatic_llr_tumor_purity + Float? filter_somatic_llr_normal_contamination_rate Int filter_minimum_depth = 1 Boolean cle_vcf_filter = false Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF"] diff --git a/definitions/detect_variants_wgs.wdl b/definitions/detect_variants_wgs.wdl index 9a6724cc..b73dba88 100644 --- a/definitions/detect_variants_wgs.wdl +++ b/definitions/detect_variants_wgs.wdl @@ -34,12 +34,12 @@ workflow detectVariantsWgs { Int? readcount_minimum_base_quality Int? readcount_minimum_mapping_quality Int scatter_count - Int varscan_strand_filter - Int varscan_min_coverage - Float varscan_min_var_freq - Float varscan_p_value + Int? varscan_strand_filter + Int? varscan_min_coverage + Float? varscan_min_var_freq + Float? varscan_p_value Float? varscan_max_normal_freq - Float fp_min_var_freq + Float? fp_min_var_freq File docm_vcf File docm_vcf_tbi Boolean filter_docm_variants = true @@ -56,9 +56,9 @@ workflow detectVariantsWgs { Float filter_gnomADe_maximum_population_allele_frequency = 0.001 Float filter_mapq0_threshold = 0.15 Int filter_minimum_depth = 1 - Float filter_somatic_llr_threshold - Float filter_somatic_llr_tumor_purity - Float filter_somatic_llr_normal_contamination_rate + Float? filter_somatic_llr_threshold + Float? filter_somatic_llr_tumor_purity + Float? filter_somatic_llr_normal_contamination_rate Boolean cle_vcf_filter = false Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF"] Array[String] variants_to_table_genotype_fields = ["GT", "AD"] diff --git a/definitions/immuno.wdl b/definitions/immuno.wdl index 16026c3e..dac8d0a9 100644 --- a/definitions/immuno.wdl +++ b/definitions/immuno.wdl @@ -156,13 +156,13 @@ workflow immuno { Int strelka_cpu_reserved = 8 Int scatter_count = 50 - Int varscan_strand_filter - Int varscan_min_coverage - Float varscan_min_var_freq - Float varscan_p_value + Int? varscan_strand_filter + Int? varscan_min_coverage + Float? varscan_min_var_freq + Float? varscan_p_value Float? varscan_max_normal_freq - Float fp_min_var_freq + Float? fp_min_var_freq File docm_vcf File docm_vcf_tbi @@ -182,9 +182,9 @@ workflow immuno { String? vep_pick Boolean cle_vcf_filter = false - Float filter_somatic_llr_threshold - Float filter_somatic_llr_tumor_purity - Float filter_somatic_llr_normal_contamination_rate + Float? filter_somatic_llr_threshold + Float? filter_somatic_llr_tumor_purity + Float? filter_somatic_llr_normal_contamination_rate Array[String] vep_to_table_fields = ["HGVSc", "HGVSp"] Array[String] variants_to_table_genotype_fields = ["GT", "AD"] diff --git a/definitions/somatic_exome.wdl b/definitions/somatic_exome.wdl index 144c8bd5..4a46ce26 100644 --- a/definitions/somatic_exome.wdl +++ b/definitions/somatic_exome.wdl @@ -56,13 +56,13 @@ workflow somaticExome { Int strelka_cpu_reserved = 8 Int scatter_count = 50 - Int varscan_strand_filter - Int varscan_min_coverage - Float varscan_min_var_freq - Float varscan_p_value + Int? varscan_strand_filter + Int? varscan_min_coverage + Float? varscan_min_var_freq + Float? varscan_p_value Float? varscan_max_normal_freq - Float fp_min_var_freq + Float? fp_min_var_freq File docm_vcf File docm_vcf_tbi @@ -72,9 +72,9 @@ workflow somaticExome { String? gnomad_field_name Float? filter_gnomADe_maximum_population_allele_frequency - Float filter_somatic_llr_threshold - Float filter_somatic_llr_tumor_purity - Float filter_somatic_llr_normal_contamination_rate + Float? filter_somatic_llr_threshold + Float? filter_somatic_llr_tumor_purity + Float? filter_somatic_llr_normal_contamination_rate File vep_cache_dir_zip String vep_ensembl_assembly diff --git a/definitions/somatic_exome_cle.wdl b/definitions/somatic_exome_cle.wdl index 2ea8577d..5b38bd67 100644 --- a/definitions/somatic_exome_cle.wdl +++ b/definitions/somatic_exome_cle.wdl @@ -46,21 +46,21 @@ workflow somaticExomeCle { Int qc_minimum_base_quality = 0 Int strelka_cpu_reserved = 8 Int scatter_count - Int varscan_strand_filter - Int varscan_min_coverage - Float varscan_min_var_freq - Float varscan_p_value + Int? varscan_strand_filter + Int? varscan_min_coverage + Float? varscan_min_var_freq + Float? varscan_p_value Float? varscan_max_normal_freq - Float fp_min_var_freq + Float? fp_min_var_freq File docm_vcf File docm_vcf_tbi String? gnomad_field_name Float? filter_gnomADe_maximum_population_allele_frequency Boolean filter_docm_variants = true Int filter_minimum_depth = 20 - Float filter_somatic_llr_threshold - Float filter_somatic_llr_tumor_purity - Float filter_somatic_llr_normal_contamination_rate + Float? filter_somatic_llr_threshold + Float? filter_somatic_llr_tumor_purity + Float? filter_somatic_llr_normal_contamination_rate File vep_cache_dir_zip String vep_ensembl_assembly String vep_ensembl_version diff --git a/definitions/somatic_exome_nonhuman.wdl b/definitions/somatic_exome_nonhuman.wdl index 6b4f2bdf..eef82cef 100644 --- a/definitions/somatic_exome_nonhuman.wdl +++ b/definitions/somatic_exome_nonhuman.wdl @@ -43,13 +43,13 @@ workflow somaticExomeNonhuman { Int strelka_cpu_reserved = 8 Int scatter_count = 50 - Int varscan_strand_filter - Int varscan_min_coverage - Float varscan_min_var_freq - Float varscan_p_value + Int? varscan_strand_filter + Int? varscan_min_coverage + Float? varscan_min_var_freq + Float? varscan_p_value Float? varscan_max_normal_freq - Float fp_min_var_freq + Float? fp_min_var_freq File vep_cache_dir_zip String vep_ensembl_assembly @@ -61,9 +61,9 @@ workflow somaticExomeNonhuman { String? vep_pick Boolean cle_vcf_filter = false - Float filter_somatic_llr_threshold - Float filter_somatic_llr_tumor_purity - Float filter_somatic_llr_normal_contamination_rate + Float? filter_somatic_llr_threshold + Float? filter_somatic_llr_tumor_purity + Float? filter_somatic_llr_normal_contamination_rate Array[String] vep_to_table_fields = ["Consequence", "SYMBOL", "Feature"] Array[String] variants_to_table_genotype_fields = ["GT", "AD"] diff --git a/definitions/somatic_wgs.wdl b/definitions/somatic_wgs.wdl index f7b64097..d68159fc 100644 --- a/definitions/somatic_wgs.wdl +++ b/definitions/somatic_wgs.wdl @@ -51,19 +51,19 @@ workflow somaticWgs { File? strelka_call_regions File? strelka_call_regions_tbi Int scatter_count - Int varscan_strand_filter - Int varscan_min_coverage - Float varscan_min_var_freq - Float varscan_p_value + Int? varscan_strand_filter + Int? varscan_min_coverage + Float? varscan_min_var_freq + Float? varscan_p_value Float? varscan_max_normal_freq - Float fp_min_var_freq + Float? fp_min_var_freq File docm_vcf File docm_vcf_tbi Boolean filter_docm_variants = true - Float filter_somatic_llr_threshold - Float filter_somatic_llr_tumor_purity - Float filter_somatic_llr_normal_contamination_rate + Float? filter_somatic_llr_threshold + Float? filter_somatic_llr_tumor_purity + Float? filter_somatic_llr_normal_contamination_rate File vep_cache_dir_zip String vep_ensembl_assembly String vep_ensembl_version diff --git a/definitions/subworkflows/mutect.wdl b/definitions/subworkflows/mutect.wdl index dc22e8c4..bf879e18 100644 --- a/definitions/subworkflows/mutect.wdl +++ b/definitions/subworkflows/mutect.wdl @@ -22,7 +22,7 @@ workflow mutect { File interval_list Int scatter_count String tumor_sample_name - Float fp_min_var_freq + Float? fp_min_var_freq } call sil.splitIntervalList { diff --git a/definitions/subworkflows/pindel.wdl b/definitions/subworkflows/pindel.wdl index 34f83567..7bcf6cd9 100644 --- a/definitions/subworkflows/pindel.wdl +++ b/definitions/subworkflows/pindel.wdl @@ -23,7 +23,7 @@ workflow pindel { String normal_sample_name Int insert_size = 400 Int scatter_count = 50 - Float fp_min_var_freq + Float? fp_min_var_freq } call siltb.splitIntervalListToBed { diff --git a/definitions/subworkflows/strelka_and_post_processing.wdl b/definitions/subworkflows/strelka_and_post_processing.wdl index ef27aa42..11f4699d 100644 --- a/definitions/subworkflows/strelka_and_post_processing.wdl +++ b/definitions/subworkflows/strelka_and_post_processing.wdl @@ -30,7 +30,7 @@ workflow strelkaAndPostProcessing { File? call_regions File? call_regions_tbi - Float fp_min_var_freq + Float? fp_min_var_freq } call s.strelka { diff --git a/definitions/subworkflows/varscan.wdl b/definitions/subworkflows/varscan.wdl index 7844e1e9..e986dcc4 100644 --- a/definitions/subworkflows/varscan.wdl +++ b/definitions/subworkflows/varscan.wdl @@ -17,10 +17,10 @@ workflow varscan { File? roi_bed - Int strand_filter - Int min_coverage - Float varscan_min_var_freq - Float p_value + Int? strand_filter + Int? min_coverage + Float? varscan_min_var_freq + Float? p_value Float? max_normal_freq } diff --git a/definitions/subworkflows/varscan_germline.wdl b/definitions/subworkflows/varscan_germline.wdl index 19e78c43..a95cd5d6 100644 --- a/definitions/subworkflows/varscan_germline.wdl +++ b/definitions/subworkflows/varscan_germline.wdl @@ -13,11 +13,11 @@ workflow varscanGermline { File reference_fai File reference_dict File interval_list - Int strand_filter - Int min_coverage - Float varscan_min_var_freq - Int min_reads - Float p_value + Int? strand_filter + Int? min_coverage + Float? varscan_min_var_freq + Int? min_reads + Float? p_value String sample_name } diff --git a/definitions/subworkflows/varscan_pre_and_post_processing.wdl b/definitions/subworkflows/varscan_pre_and_post_processing.wdl index c3038891..6c4d98c5 100644 --- a/definitions/subworkflows/varscan_pre_and_post_processing.wdl +++ b/definitions/subworkflows/varscan_pre_and_post_processing.wdl @@ -26,10 +26,10 @@ workflow varscanPreAndPostProcessing { File interval_list - Int strand_filter - Int min_coverage - Float varscan_min_var_freq - Float p_value + Int? strand_filter + Int? min_coverage + Float? varscan_min_var_freq + Float? p_value Float? max_normal_freq Int scatter_count = 50 } diff --git a/definitions/tumor_only_detect_variants.wdl b/definitions/tumor_only_detect_variants.wdl index f53c833e..85df8cd5 100644 --- a/definitions/tumor_only_detect_variants.wdl +++ b/definitions/tumor_only_detect_variants.wdl @@ -31,11 +31,11 @@ workflow tumorOnlyDetectVariants { String gnomad_field_name = "gnomADe_AF" # only change with gnomad_filter_annotation File roi_intervals - Int varscan_strand_filter - Int varscan_min_coverage - Int varscan_min_reads - Float varscan_min_var_freq - Float varscan_p_value + Int? varscan_strand_filter + Int? varscan_min_coverage + Int? varscan_min_reads + Float? varscan_min_var_freq + Float? varscan_p_value Float maximum_population_allele_frequency = 0.001 File vep_cache_dir_zip diff --git a/definitions/tumor_only_exome.wdl b/definitions/tumor_only_exome.wdl index c4d30ffc..2ee65f60 100644 --- a/definitions/tumor_only_exome.wdl +++ b/definitions/tumor_only_exome.wdl @@ -34,12 +34,12 @@ workflow tumorOnlyExome { File omni_vcf_tbi String picard_metric_accumulation_level Int target_interval_padding = 100 - Int varscan_strand_filter - Int varscan_min_coverage - Float varscan_min_var_freq - Float varscan_p_value - Int varscan_min_reads - Float fp_min_var_freq + Int? varscan_strand_filter + Int? varscan_min_coverage + Float? varscan_min_var_freq + Float? varscan_p_value + Int? varscan_min_reads + Float? fp_min_var_freq Float maximum_population_allele_frequency = 0.001 File vep_cache_dir_zip diff --git a/definitions/tumor_only_wgs.wdl b/definitions/tumor_only_wgs.wdl index f6a75f2e..f09755d8 100644 --- a/definitions/tumor_only_wgs.wdl +++ b/definitions/tumor_only_wgs.wdl @@ -58,9 +58,9 @@ workflow tumorOnlyWgs { Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT", "set", "AC", "AF"] Array[String] variants_to_table_genotype_fields = ["GT", "AD"] Array[String] vep_to_table_fields = ["HGVSc", "HGVSp"] - Int varscan_min_coverage - Float varscan_min_var_freq - Int varscan_min_reads + Int? varscan_min_coverage + Float? varscan_min_var_freq + Int? varscan_min_reads Float maximum_population_allele_frequency = 0.001 } From 3041349e68089e8a3211bfe3a8a49aa6c593efc8 Mon Sep 17 00:00:00 2001 From: Malachi Griffith Date: Fri, 21 Apr 2023 10:46:03 -0500 Subject: [PATCH 09/10] fix missing default on input --- definitions/subworkflows/filter_vcf.wdl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/definitions/subworkflows/filter_vcf.wdl b/definitions/subworkflows/filter_vcf.wdl index 8940a0ad..dbfc01cb 100644 --- a/definitions/subworkflows/filter_vcf.wdl +++ b/definitions/subworkflows/filter_vcf.wdl @@ -18,9 +18,9 @@ workflow filterVcf { File tumor_bam File tumor_bam_bai Boolean do_cle_vcf_filter - Float filter_somatic_llr_threshold - Float filter_somatic_llr_tumor_purity - Float filter_somatic_llr_normal_contamination_rate + Float? filter_somatic_llr_threshold + Float? filter_somatic_llr_tumor_purity + Float? filter_somatic_llr_normal_contamination_rate File reference File reference_fai File reference_dict From 35df3edcec07588247434f83c9f2a75be09a3ece Mon Sep 17 00:00:00 2001 From: Malachi Griffith Date: Fri, 21 Apr 2023 10:54:35 -0500 Subject: [PATCH 10/10] fix another missing default on inputs --- definitions/subworkflows/filter_vcf_nonhuman.wdl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/definitions/subworkflows/filter_vcf_nonhuman.wdl b/definitions/subworkflows/filter_vcf_nonhuman.wdl index 7b928d98..acb52ca2 100644 --- a/definitions/subworkflows/filter_vcf_nonhuman.wdl +++ b/definitions/subworkflows/filter_vcf_nonhuman.wdl @@ -13,9 +13,9 @@ workflow filterVcfNonhuman { File tumor_bam File tumor_bam_bai Boolean do_cle_vcf_filter - Float filter_somatic_llr_threshold - Float filter_somatic_llr_tumor_purity - Float filter_somatic_llr_normal_contamination_rate + Float? filter_somatic_llr_threshold + Float? filter_somatic_llr_tumor_purity + Float? filter_somatic_llr_normal_contamination_rate File reference File reference_fai File reference_dict