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cle_aml_trio.cwl
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cle_aml_trio.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Replace legacy AML Trio Assay"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference: string
tumor_sequence:
type: ../types/sequence_data.yml#sequence_data[]
tumor_name:
type: string?
default: 'tumor'
normal_sequence:
type: ../types/sequence_data.yml#sequence_data[]
normal_name:
type: string?
default: 'normal'
followup_sequence:
type: ../types/sequence_data.yml#sequence_data[]
followup_name:
type: string?
default: 'followup'
mills:
type: File
secondaryFiles: [.tbi]
known_indels:
type: File
secondaryFiles: [.tbi]
dbsnp_vcf:
type: File
secondaryFiles: [.tbi]
bqsr_intervals:
type: string[]
bait_intervals:
type: File
target_intervals:
type: File
per_base_intervals:
type: ../types/labelled_file.yml#labelled_file[]
per_target_intervals:
type: ../types/labelled_file.yml#labelled_file[]
summary_intervals:
type: ../types/labelled_file.yml#labelled_file[]
omni_vcf:
type: File
secondaryFiles: [.tbi]
emit_reference_confidence:
type: string
gvcf_gq_bands:
type: string[]
intervals:
type:
type: array
items:
type: array
items: string
variant_reporting_intervals:
type: File
picard_metric_accumulation_level:
type: string
qc_minimum_mapping_quality:
type: int?
default: 0
qc_minimum_base_quality:
type: int?
default: 0
interval_list:
type: File
cosmic_vcf:
type: File?
secondaryFiles: [.tbi]
panel_of_normals_vcf:
type: File?
secondaryFiles: [.tbi]
strelka_cpu_reserved:
type: int?
default: 8
mutect_scatter_count:
type: int
mutect_artifact_detection_mode:
type: boolean
default: false
mutect_max_alt_allele_in_normal_fraction:
type: float?
mutect_max_alt_alleles_in_normal_count:
type: int?
varscan_strand_filter:
type: int?
default: 0
varscan_min_coverage:
type: int?
default: 8
varscan_min_var_freq:
type: float?
default: 0.05
varscan_p_value:
type: float?
default: 0.99
varscan_max_normal_freq:
type: float?
pindel_region_file:
type: File
pindel_insert_size:
type: int
default: 400
docm_vcf:
type: File
secondaryFiles: [.tbi]
filter_docm_variants:
type: boolean?
default: true
filter_minimum_depth:
type: int?
default: 20
vep_cache_dir:
type: string
synonyms_file:
type: File?
annotate_coding_only:
type: boolean?
germline_coding_only:
type: boolean?
vep_pick:
type:
- "null"
- type: enum
symbols: ["pick", "flag_pick", "pick_allele", "per_gene", "pick_allele_gene", "flag_pick_allele", "flag_pick_allele_gene"]
cle_vcf_filter:
type: boolean
default: true
variants_to_table_fields:
type: string[]
default: [CHROM,POS,ID,REF,ALT,set,AC,AF]
variants_to_table_genotype_fields:
type: string[]
default: [GT,AD]
vep_to_table_fields:
type: string[]
default: [HGVSc,HGVSp]
vep_ensembl_assembly:
type: string
doc: "genome assembly to use in vep. Examples: GRCh38 or GRCm38"
vep_ensembl_version:
type: string
doc: "ensembl version - Must be present in the cache directory. Example: 95"
vep_ensembl_species:
type: string
doc: "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus"
somalier_vcf:
type: File
custom_gnomad_vcf:
type: File?
secondaryFiles: [.tbi]
custom_clinvar_vcf:
type: File?
secondaryFiles: [.tbi]
germline_tsv_prefix:
type: string?
default: 'germline_variants'
germline_variants_to_table_fields:
type: string[]
default: [CHROM,POS,ID,REF,ALT,AC,AF]
germline_variants_to_table_genotype_fields:
type: string[]
default: [GT,AD]
germline_vep_to_table_fields:
type: string[]
default: [HGVSc,HGVSp]
disclaimer_text:
type: string?
default: "This laboratory developed test (LDT) was developed and its performance characteristics determined by the CLIA Licensed Environment laboratory at the McDonnell Genome Institute at Washington University (MGI-CLE, CLIA #26D2092546, CAP #9047655), Dr. David H. Spencer MD, PhD, FCAP, Medical Director. 4444 Forest Park Avenue, Rm 4127 St. Louis, Missouri 63108 (314) 286-1460 Fax: (314) 286-1810. The MGI-CLE laboratory is regulated under CLIA as certified to perform high-complexity testing. This test has not been cleared or approved by the FDA."
outputs:
tumor_cram:
type: File
outputSource: tumor_index_cram/indexed_cram
tumor_mark_duplicates_metrics:
type: File
outputSource: tumor_alignment_and_qc/mark_duplicates_metrics
tumor_insert_size_metrics:
type: File
outputSource: tumor_alignment_and_qc/insert_size_metrics
tumor_alignment_summary_metrics:
type: File
outputSource: tumor_alignment_and_qc/alignment_summary_metrics
tumor_hs_metrics:
type: File
outputSource: tumor_alignment_and_qc/hs_metrics
tumor_summary_hs_metrics:
type: File[]
outputSource: tumor_alignment_and_qc/summary_hs_metrics
tumor_flagstats:
type: File
outputSource: tumor_alignment_and_qc/flagstats
tumor_verify_bam_id_metrics:
type: File
outputSource: tumor_alignment_and_qc/verify_bam_id_metrics
tumor_verify_bam_id_depth:
type: File
outputSource: tumor_alignment_and_qc/verify_bam_id_depth
normal_cram:
type: File
outputSource: normal_index_cram/indexed_cram
normal_mark_duplicates_metrics:
type: File
outputSource: normal_alignment_and_qc/mark_duplicates_metrics
normal_insert_size_metrics:
type: File
outputSource: normal_alignment_and_qc/insert_size_metrics
normal_alignment_summary_metrics:
type: File
outputSource: normal_alignment_and_qc/alignment_summary_metrics
normal_hs_metrics:
type: File
outputSource: normal_alignment_and_qc/hs_metrics
normal_summary_hs_metrics:
type: File[]
outputSource: normal_alignment_and_qc/summary_hs_metrics
normal_flagstats:
type: File
outputSource: normal_alignment_and_qc/flagstats
normal_verify_bam_id_metrics:
type: File
outputSource: normal_alignment_and_qc/verify_bam_id_metrics
normal_verify_bam_id_depth:
type: File
outputSource: normal_alignment_and_qc/verify_bam_id_depth
followup_cram:
type: File
outputSource: followup_index_cram/indexed_cram
followup_mark_duplicates_metrics:
type: File
outputSource: followup_alignment_and_qc/mark_duplicates_metrics
followup_insert_size_metrics:
type: File
outputSource: followup_alignment_and_qc/insert_size_metrics
followup_alignment_summary_metrics:
type: File
outputSource: followup_alignment_and_qc/alignment_summary_metrics
followup_hs_metrics:
type: File
outputSource: followup_alignment_and_qc/hs_metrics
followup_summary_hs_metrics:
type: File[]
outputSource: followup_alignment_and_qc/summary_hs_metrics
followup_flagstats:
type: File
outputSource: followup_alignment_and_qc/flagstats
followup_verify_bam_id_metrics:
type: File
outputSource: followup_alignment_and_qc/verify_bam_id_metrics
followup_verify_bam_id_depth:
type: File
outputSource: followup_alignment_and_qc/verify_bam_id_depth
mutect_unfiltered_vcf:
type: File
outputSource: tumor_detect_variants/mutect_unfiltered_vcf
secondaryFiles: [.tbi]
mutect_filtered_vcf:
type: File
outputSource: tumor_detect_variants/mutect_filtered_vcf
secondaryFiles: [.tbi]
strelka_unfiltered_vcf:
type: File
outputSource: tumor_detect_variants/strelka_unfiltered_vcf
secondaryFiles: [.tbi]
strelka_filtered_vcf:
type: File
outputSource: tumor_detect_variants/strelka_filtered_vcf
secondaryFiles: [.tbi]
varscan_unfiltered_vcf:
type: File
outputSource: tumor_detect_variants/varscan_unfiltered_vcf
secondaryFiles: [.tbi]
varscan_filtered_vcf:
type: File
outputSource: tumor_detect_variants/varscan_filtered_vcf
secondaryFiles: [.tbi]
pindel_unfiltered_vcf:
type: File
outputSource: tumor_detect_variants/pindel_unfiltered_vcf
secondaryFiles: [.tbi]
pindel_filtered_vcf:
type: File
outputSource: tumor_detect_variants/pindel_filtered_vcf
secondaryFiles: [.tbi]
docm_filtered_vcf:
type: File
outputSource: tumor_detect_variants/docm_filtered_vcf
secondaryFiles: [.tbi]
pindel_region_vcf:
type: File
outputSource: pindel_region/pindel_region_vcf
secondaryFiles: [.tbi]
tumor_snv_bam_readcount_tsv:
type: File
outputSource: tumor_detect_variants/tumor_snv_bam_readcount_tsv
tumor_indel_bam_readcount_tsv:
type: File
outputSource: tumor_detect_variants/tumor_indel_bam_readcount_tsv
normal_snv_bam_readcount_tsv:
type: File
outputSource: tumor_detect_variants/normal_snv_bam_readcount_tsv
normal_indel_bam_readcount_tsv:
type: File
outputSource: tumor_detect_variants/normal_indel_bam_readcount_tsv
followup_snv_bam_readcount_tsv:
type: File
outputSource: followup_bam_readcount/snv_bam_readcount_tsv
followup_indel_bam_readcount_tsv:
type: File
outputSource: followup_bam_readcount/indel_bam_readcount_tsv
tumor_final_vcf:
type: File
outputSource: tumor_detect_variants/final_vcf
secondaryFiles: [.tbi]
tumor_final_filtered_vcf:
type: File
outputSource: tumor_detect_variants/final_filtered_vcf
secondaryFiles: [.tbi]
tumor_final_tsv:
type: File
outputSource: add_disclaimer_to_tumor_final_tsv/output_file
tumor_vep_summary:
type: File
outputSource: tumor_detect_variants/vep_summary
germline_final_vcf:
type: File
outputSource: germline_detect_variants/final_vcf
secondaryFiles: [.tbi]
germline_coding_vcf:
type: File
outputSource: germline_detect_variants/coding_vcf
secondaryFiles: [.tbi]
germline_limited_vcf:
type: File
outputSource: germline_detect_variants/limited_vcf
secondaryFiles: [.tbi]
germline_final_tsv:
type: File
outputSource: add_disclaimer_to_germline_final_tsv/output_file
somalier_concordance_metrics:
type: File
outputSource: concordance/somalier_pairs
somalier_concordance_statistics:
type: File
outputSource: concordance/somalier_samples
alignment_stat_report:
type: File
outputSource: alignment_stat_report/alignment_stat
coverage_stat_report:
type: File
outputSource: coverage_stat_report/coverage_stat
full_variant_report:
type: File
outputSource: add_disclaimer_to_full_variant_report/output_file
steps:
normal_alignment_and_qc:
run: exome_alignment.cwl
in:
reference: reference
sequence: normal_sequence
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
bqsr_intervals: bqsr_intervals
bait_intervals: bait_intervals
target_intervals: target_intervals
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
omni_vcf: omni_vcf
picard_metric_accumulation_level: picard_metric_accumulation_level
minimum_mapping_quality: qc_minimum_mapping_quality
minimum_base_quality: qc_minimum_base_quality
final_name:
source: normal_name
valueFrom: "$(self).bam"
out:
[bam, mark_duplicates_metrics, insert_size_metrics, alignment_summary_metrics, hs_metrics, summary_hs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]
tumor_alignment_and_qc:
run: exome_alignment.cwl
in:
reference: reference
sequence: tumor_sequence
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
bqsr_intervals: bqsr_intervals
bait_intervals: bait_intervals
target_intervals: target_intervals
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
omni_vcf: omni_vcf
picard_metric_accumulation_level: picard_metric_accumulation_level
minimum_mapping_quality: qc_minimum_mapping_quality
minimum_base_quality: qc_minimum_base_quality
final_name:
source: tumor_name
valueFrom: "$(self).bam"
out:
[bam, mark_duplicates_metrics, insert_size_metrics, alignment_summary_metrics, hs_metrics, summary_hs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]
followup_alignment_and_qc:
run: exome_alignment.cwl
in:
reference: reference
sequence: followup_sequence
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
bqsr_intervals: bqsr_intervals
bait_intervals: bait_intervals
target_intervals: target_intervals
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
omni_vcf: omni_vcf
picard_metric_accumulation_level: picard_metric_accumulation_level
minimum_mapping_quality: qc_minimum_mapping_quality
minimum_base_quality: qc_minimum_base_quality
final_name:
source: followup_name
valueFrom: "$(self).bam"
out:
[bam, mark_duplicates_metrics, insert_size_metrics, alignment_summary_metrics, hs_metrics, summary_hs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]
concordance:
run: ../tools/concordance.cwl
in:
reference: reference
bam_1: tumor_alignment_and_qc/bam
bam_2: normal_alignment_and_qc/bam
bam_3: followup_alignment_and_qc/bam
vcf: somalier_vcf
out:
[somalier_pairs, somalier_samples]
tumor_detect_variants:
run: detect_variants.cwl
in:
reference: reference
tumor_bam: tumor_alignment_and_qc/bam
normal_bam: normal_alignment_and_qc/bam
interval_list: interval_list
dbsnp_vcf: dbsnp_vcf
cosmic_vcf: cosmic_vcf
panel_of_normals_vcf: panel_of_normals_vcf
strelka_exome_mode:
default: true
strelka_cpu_reserved: strelka_cpu_reserved
mutect_scatter_count: mutect_scatter_count
mutect_artifact_detection_mode: mutect_artifact_detection_mode
mutect_max_alt_allele_in_normal_fraction: mutect_max_alt_allele_in_normal_fraction
mutect_max_alt_alleles_in_normal_count: mutect_max_alt_alleles_in_normal_count
varscan_strand_filter: varscan_strand_filter
varscan_min_coverage: varscan_min_coverage
varscan_min_var_freq: varscan_min_var_freq
varscan_p_value: varscan_p_value
varscan_max_normal_freq: varscan_max_normal_freq
pindel_insert_size: pindel_insert_size
docm_vcf: docm_vcf
filter_docm_variants: filter_docm_variants
filter_minimum_depth: filter_minimum_depth
vep_ensembl_assembly: vep_ensembl_assembly
vep_ensembl_version: vep_ensembl_version
vep_ensembl_species: vep_ensembl_species
vep_cache_dir: vep_cache_dir
synonyms_file: synonyms_file
annotate_coding_only: annotate_coding_only
vep_pick: vep_pick
cle_vcf_filter: cle_vcf_filter
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
custom_gnomad_vcf: custom_gnomad_vcf
custom_clinvar_vcf: custom_clinvar_vcf
out:
[mutect_unfiltered_vcf, mutect_filtered_vcf, strelka_unfiltered_vcf, strelka_filtered_vcf, varscan_unfiltered_vcf, varscan_filtered_vcf, pindel_unfiltered_vcf, pindel_filtered_vcf, docm_filtered_vcf, final_vcf, final_filtered_vcf, final_tsv, vep_summary, tumor_snv_bam_readcount_tsv, tumor_indel_bam_readcount_tsv, normal_snv_bam_readcount_tsv, normal_indel_bam_readcount_tsv]
add_disclaimer_to_tumor_final_tsv:
run: ../tools/add_string_at_line.cwl
in:
input_file: tumor_detect_variants/final_tsv
line_number:
default: 1
some_text: disclaimer_text
out:
[output_file]
pindel_region:
run: ../subworkflows/pindel_region.cwl
in:
reference: reference
tumor_bam: tumor_alignment_and_qc/bam
normal_bam: normal_alignment_and_qc/bam
region_file: pindel_region_file
insert_size: pindel_insert_size
out:
[pindel_region_vcf]
followup_bam_readcount:
run: ../tools/bam_readcount.cwl
in:
vcf: tumor_detect_variants/final_filtered_vcf
sample:
default: 'TUMOR'
reference_fasta: reference
bam: followup_alignment_and_qc/bam
prefix: followup_name
out:
[snv_bam_readcount_tsv, indel_bam_readcount_tsv]
extract_freemix:
in:
verify_bam_id_metrics: normal_alignment_and_qc/verify_bam_id_metrics
out:
[freemix_score]
run:
class: ExpressionTool
requirements:
- class: InlineJavascriptRequirement
inputs:
verify_bam_id_metrics:
type: File
inputBinding:
loadContents: true
outputs:
freemix_score:
type: string?
expression: |
${
var metrics = inputs.verify_bam_id_metrics.contents.split("\n");
if ( metrics[0].split("\t")[6] == 'FREEMIX' ) {
return {'freemix_score': metrics[1].split("\t")[6]};
} else {
return {'freemix_score:': null };
}
}
germline_detect_variants:
run: ../subworkflows/germline_detect_variants.cwl
in:
reference: reference
bam: normal_alignment_and_qc/bam
emit_reference_confidence: emit_reference_confidence
gvcf_gq_bands: gvcf_gq_bands
intervals: intervals
contamination_fraction: extract_freemix/freemix_score
vep_cache_dir: vep_cache_dir
vep_ensembl_assembly: vep_ensembl_assembly
vep_ensembl_version: vep_ensembl_version
vep_ensembl_species: vep_ensembl_species
synonyms_file: synonyms_file
annotate_coding_only: germline_coding_only
custom_gnomad_vcf: custom_gnomad_vcf
limit_variant_intervals: variant_reporting_intervals
custom_clinvar_vcf: custom_clinvar_vcf
variants_to_table_fields: germline_variants_to_table_fields
variants_to_table_genotype_fields: germline_variants_to_table_genotype_fields
vep_to_table_fields: germline_vep_to_table_fields
final_tsv_prefix: germline_tsv_prefix
out:
[final_vcf, coding_vcf, limited_vcf, final_tsv]
add_disclaimer_to_germline_final_tsv:
run: ../tools/add_string_at_line.cwl
in:
input_file: germline_detect_variants/final_tsv
line_number:
default: 1
some_text: disclaimer_text
out:
[output_file]
alignment_stat_report:
run: ../tools/cle_aml_trio_report_alignment_stat.cwl
in:
normal_alignment_summary_metrics: normal_alignment_and_qc/alignment_summary_metrics
tumor_alignment_summary_metrics: tumor_alignment_and_qc/alignment_summary_metrics
followup_alignment_summary_metrics: followup_alignment_and_qc/alignment_summary_metrics
out:
[alignment_stat]
coverage_stat_report:
run: ../tools/cle_aml_trio_report_coverage_stat.cwl
in:
normal_roi_hs_metrics: normal_alignment_and_qc/hs_metrics
normal_summary_hs_metrics: [normal_alignment_and_qc/summary_hs_metrics]
tumor_roi_hs_metrics: tumor_alignment_and_qc/hs_metrics
tumor_summary_hs_metrics: [tumor_alignment_and_qc/summary_hs_metrics]
followup_roi_hs_metrics: followup_alignment_and_qc/hs_metrics
followup_summary_hs_metrics: [followup_alignment_and_qc/summary_hs_metrics]
out:
[coverage_stat]
full_variant_report:
run: ../tools/cle_aml_trio_report_full_variants.cwl
in:
variant_tsv: tumor_detect_variants/final_tsv
followup_snv_bam_readcount: followup_bam_readcount/snv_bam_readcount_tsv
followup_indel_bam_readcount: followup_bam_readcount/indel_bam_readcount_tsv
pindel_region_vcf: pindel_region/pindel_region_vcf
out:
[full_variant_report]
add_disclaimer_to_full_variant_report:
run: ../tools/add_string_at_line.cwl
in:
input_file: full_variant_report/full_variant_report
line_number:
default: 1
some_text: disclaimer_text
out:
[output_file]
normal_bam_to_cram:
run: ../tools/bam_to_cram.cwl
in:
bam: normal_alignment_and_qc/bam
reference: reference
out:
[cram]
normal_index_cram:
run: ../tools/index_cram.cwl
in:
cram: normal_bam_to_cram/cram
out:
[indexed_cram]
tumor_bam_to_cram:
run: ../tools/bam_to_cram.cwl
in:
bam: tumor_alignment_and_qc/bam
reference: reference
out:
[cram]
tumor_index_cram:
run: ../tools/index_cram.cwl
in:
cram: tumor_bam_to_cram/cram
out:
[indexed_cram]
followup_bam_to_cram:
run: ../tools/bam_to_cram.cwl
in:
bam: followup_alignment_and_qc/bam
reference: reference
out:
[cram]
followup_index_cram:
run: ../tools/index_cram.cwl
in:
cram: followup_bam_to_cram/cram
out:
[indexed_cram]