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Merge pull request #136 from tmooney/pr110
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Variant Parameter Cleanup (from PR#110)
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@malachig
malachig authored Nov 14, 2023
2 parents 80bf6f6 + 35df3ed commit 2f7620e
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Showing 24 changed files with 157 additions and 119 deletions.
24 changes: 14 additions & 10 deletions definitions/detect_variants.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -65,9 +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"]
Expand All @@ -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 {
Expand All @@ -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 {
Expand All @@ -121,7 +125,7 @@ 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,
normal_sample_name=normal_sample_name,
Expand Down
24 changes: 14 additions & 10 deletions definitions/detect_variants_nonhuman.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -53,9 +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"]
Expand All @@ -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 {
Expand All @@ -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 {
Expand All @@ -106,7 +110,7 @@ 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,
normal_sample_name=normal_sample_name,
Expand Down
23 changes: 13 additions & 10 deletions definitions/detect_variants_wgs.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -55,9 +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"]
Expand All @@ -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 {
Expand All @@ -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 {
Expand All @@ -122,7 +125,7 @@ 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
}
Expand Down
19 changes: 15 additions & 4 deletions definitions/immuno.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -179,6 +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"]
Expand Down Expand Up @@ -333,6 +340,7 @@ 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,
Expand All @@ -344,6 +352,9 @@ 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,
Expand Down
17 changes: 10 additions & 7 deletions definitions/somatic_exome.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -70,9 +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
Expand Down Expand Up @@ -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,
Expand Down
16 changes: 9 additions & 7 deletions definitions/somatic_exome_cle.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -46,20 +46,21 @@ 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
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
Expand Down Expand Up @@ -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,
Expand Down
17 changes: 10 additions & 7 deletions definitions/somatic_exome_nonhuman.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -59,9 +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"]
Expand Down Expand Up @@ -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,
Expand Down
17 changes: 9 additions & 8 deletions definitions/somatic_wgs.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -51,19 +51,19 @@ 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
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
Expand Down Expand Up @@ -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,
Expand Down
6 changes: 3 additions & 3 deletions definitions/subworkflows/filter_vcf.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
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