/
aml_trio_cle_gathered.cwl
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aml_trio_cle_gathered.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "gather AML trio outputs"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- $import: ../types/vep_custom_annotation.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:
type: enum
symbols: ['NONE', 'BP_RESOLUTION', 'GVCF']
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
strelka_cpu_reserved:
type: int?
default: 8
mutect_scatter_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
- Directory
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"
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_custom_annotations:
type: ../types/vep_custom_annotation.yml#vep_custom_annotation[]
doc: "custom type, check types directory for input format"
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]
somalier_vcf:
type: File
output_dir:
type: string
disclaimer_version:
type: string
tumor_sample_name:
type: string
normal_sample_name:
type: string
disclaimer_text:
type: string?
outputs:
final_outputs:
type: string[]
outputSource: gatherer/gathered_files
steps:
aml_trio:
run: aml_trio_cle.cwl
in:
reference: reference
tumor_sequence: tumor_sequence
tumor_name: tumor_name
normal_sequence: normal_sequence
normal_name: normal_name
followup_sequence: followup_sequence
followup_name: followup_name
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
emit_reference_confidence: emit_reference_confidence
gvcf_gq_bands: gvcf_gq_bands
intervals: intervals
variant_reporting_intervals: variant_reporting_intervals
picard_metric_accumulation_level: picard_metric_accumulation_level
qc_minimum_mapping_quality: qc_minimum_mapping_quality
qc_minimum_base_quality: qc_minimum_base_quality
interval_list: interval_list
strelka_cpu_reserved: strelka_cpu_reserved
mutect_scatter_count: mutect_scatter_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_region_file: pindel_region_file
pindel_insert_size: pindel_insert_size
docm_vcf: docm_vcf
filter_docm_variants: filter_docm_variants
filter_minimum_depth: filter_minimum_depth
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: annotate_coding_only
germline_coding_only: germline_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
vep_custom_annotations: vep_custom_annotations
somalier_vcf: somalier_vcf
germline_tsv_prefix: germline_tsv_prefix
germline_variants_to_table_fields: germline_variants_to_table_fields
germline_variants_to_table_genotype_fields: germline_variants_to_table_genotype_fields
germline_vep_to_table_fields: germline_vep_to_table_fields
disclaimer_version: disclaimer_version
tumor_sample_name: tumor_sample_name
normal_sample_name: normal_sample_name
disclaimer_text: disclaimer_text
out:
[tumor_cram, tumor_mark_duplicates_metrics, tumor_insert_size_metrics, tumor_alignment_summary_metrics, tumor_hs_metrics, tumor_summary_hs_metrics, tumor_flagstats, tumor_verify_bam_id_metrics, tumor_verify_bam_id_depth, normal_cram, normal_mark_duplicates_metrics, normal_insert_size_metrics, normal_alignment_summary_metrics, normal_hs_metrics, normal_summary_hs_metrics, normal_flagstats, normal_verify_bam_id_metrics, normal_verify_bam_id_depth, followup_cram, followup_mark_duplicates_metrics, followup_insert_size_metrics, followup_alignment_summary_metrics, followup_hs_metrics, followup_summary_hs_metrics, followup_flagstats, followup_verify_bam_id_metrics, followup_verify_bam_id_depth, 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, pindel_region_vcf, tumor_final_vcf, tumor_final_filtered_vcf, tumor_final_tsv, tumor_vep_summary, germline_final_vcf, germline_filtered_vcf, germline_final_tsv, germline_filtered_tsv, alignment_stat_report, coverage_stat_report, full_variant_report, tumor_snv_bam_readcount_tsv, tumor_indel_bam_readcount_tsv, normal_snv_bam_readcount_tsv, normal_indel_bam_readcount_tsv, followup_snv_bam_readcount_tsv, followup_indel_bam_readcount_tsv, somalier_concordance_metrics, somalier_concordance_statistics]
gatherer:
run: ../tools/gatherer.cwl
in:
output_dir: output_dir
all_files:
source: [aml_trio/tumor_cram, aml_trio/tumor_mark_duplicates_metrics, aml_trio/tumor_insert_size_metrics, aml_trio/tumor_alignment_summary_metrics, aml_trio/tumor_hs_metrics, aml_trio/tumor_summary_hs_metrics, aml_trio/tumor_flagstats, aml_trio/tumor_verify_bam_id_metrics, aml_trio/tumor_verify_bam_id_depth, aml_trio/normal_cram, aml_trio/normal_mark_duplicates_metrics, aml_trio/normal_insert_size_metrics, aml_trio/normal_alignment_summary_metrics, aml_trio/normal_hs_metrics, aml_trio/normal_summary_hs_metrics, aml_trio/normal_flagstats, aml_trio/normal_verify_bam_id_metrics, aml_trio/normal_verify_bam_id_depth, aml_trio/followup_cram, aml_trio/followup_mark_duplicates_metrics, aml_trio/followup_insert_size_metrics, aml_trio/followup_alignment_summary_metrics, aml_trio/followup_hs_metrics, aml_trio/followup_summary_hs_metrics, aml_trio/followup_flagstats, aml_trio/followup_verify_bam_id_metrics, aml_trio/followup_verify_bam_id_depth, aml_trio/mutect_unfiltered_vcf, aml_trio/mutect_filtered_vcf, aml_trio/strelka_unfiltered_vcf, aml_trio/strelka_filtered_vcf, aml_trio/varscan_unfiltered_vcf, aml_trio/varscan_filtered_vcf, aml_trio/pindel_unfiltered_vcf, aml_trio/pindel_filtered_vcf, aml_trio/docm_filtered_vcf, aml_trio/pindel_region_vcf, aml_trio/tumor_final_vcf, aml_trio/tumor_final_filtered_vcf, aml_trio/tumor_final_tsv, aml_trio/tumor_vep_summary, aml_trio/germline_final_vcf, aml_trio/germline_filtered_vcf, aml_trio/germline_final_tsv, aml_trio/germline_filtered_tsv, aml_trio/alignment_stat_report, aml_trio/coverage_stat_report, aml_trio/full_variant_report, aml_trio/tumor_snv_bam_readcount_tsv, aml_trio/tumor_indel_bam_readcount_tsv, aml_trio/normal_snv_bam_readcount_tsv, aml_trio/normal_indel_bam_readcount_tsv, aml_trio/followup_snv_bam_readcount_tsv, aml_trio/followup_indel_bam_readcount_tsv, aml_trio/somalier_concordance_metrics, aml_trio/somalier_concordance_statistics]
valueFrom: ${
function flatten(inArr, outArr) {
var arrLen = inArr.length;
for (var i = 0; i < arrLen; i++) {
if (Array.isArray(inArr[i])) {
flatten(inArr[i], outArr);
}
else {
outArr.push(inArr[i]);
}
}
return outArr;
}
var no_secondaries = flatten(self, []);
var all_files = [];
var arrLen = no_secondaries.length;
for (var i = 0; i < arrLen; i++) {
all_files.push(no_secondaries[i]);
var secondaryLen = no_secondaries[i].secondaryFiles.length;
for (var j = 0; j < secondaryLen; j++) {
all_files.push(no_secondaries[i].secondaryFiles[j]);
}
}
return all_files;
}
out: [gathered_files]