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snps_and_indels.cwl
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snps_and_indels.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
SubworkflowFeatureRequirement: {}
ScatterFeatureRequirement: {}
InlineJavascriptRequirement: {}
SchemaDefRequirement:
types:
- $import: ../../resources/schemas/variants_tools.yaml
- $import: ../../resources/schemas/params/mutect.yaml
- $import: ../../resources/schemas/params/vardict.yaml
- $import: ../../resources/schemas/params/bcftools.yaml
- $import: ../../resources/schemas/params/basic-filtering-mutect.yaml
- $import: ../../resources/schemas/params/basic-filtering-vardict.yaml
- $import: ../../resources/schemas/params/vcf2maf.yaml
- $import: ../../resources/schemas/params/gbcms_params.yaml
- $import: ../../resources/schemas/params/access_filters.yaml
# - $import: ../../resources/run_tools/traceback.yaml
inputs:
project_name: string
version: string
run_tools: ../../resources/schemas/variants_tools.yaml#run_tools
# traceback: ../../resources/run_tools/traceback.yaml#traceback
mutect_params: ../../resources/schemas/params/mutect.yaml#mutect_params
vardict_params: ../../resources/schemas/params/vardict.yaml#vardict_params
bcftools_params: ../../resources/schemas/params/bcftools.yaml#bcftools_params
basicfiltering_mutect_params: ../../resources/schemas/params/basic-filtering-mutect.yaml#basicfiltering_mutect_params
basicfiltering_vardict_params: ../../resources/schemas/params/basic-filtering-vardict.yaml#basicfiltering_vardict_params
vcf2maf_params: ../../resources/schemas/params/vcf2maf.yaml#vcf2maf_params
gbcms_params: ../../resources/schemas/params/gbcms_params.yaml#gbcms_params
access_filters_params: ../../resources/schemas/params/access_filters.yaml#access_filters__params
hotspots: File
blacklist_file: File
custom_enst_file: File
annotate_concat_header_file: File
# Todo: get traceback to work
# title_file: File
#########################################
# Tumor bams should be sorted in paired #
# order with Normal bams #
#########################################
tumor_bams:
type: File[]
secondaryFiles: [^.bai]
normal_bams:
type: File[]
secondaryFiles: [^.bai]
genotyping_bams:
type: File[]
secondaryFiles: [^.bai]
# traceback_bams:
# type: File[]
# secondaryFiles: [^.bai]
tumor_sample_names: string[]
normal_sample_names: string[]
genotyping_bams_ids: string[]
matched_normal_ids: string[]
# traceback_sample_ids: string[]
# traceback_mutation_file: File
bed_file: File
dbsnp:
type: File
secondaryFiles: [.idx]
cosmic:
type: File
secondaryFiles: [.idx]
ref_fasta:
type: File
secondaryFiles: [.fai, ^.dict]
exac_filter:
type: File
secondaryFiles:
- .tbi
outputs:
concatenated_vcf:
type: File[]
outputSource: module_3/concatenated_vcf
annotated_concatenated_vcf:
type: File[]
outputSource: module_3/annotated_concatenated_vcf
mutect_vcf:
type: File[]
outputSource: module_3/mutect_vcf
mutect_callstats:
type: File[]
outputSource: module_3/mutect_callstats
vardict_vcf:
type: File[]
outputSource: module_3/vardict_vcf
mutect_normalized_vcf:
type: File[]
outputSource: module_3/mutect_normalized_vcf
vardict_normalized_vcf:
type: File[]
outputSource: module_3/vardict_normalized_vcf
final_maf:
type: File[]
outputSource: module_4/maf
kept_rmvbyanno_maf:
type: File[]
outputSource: module_4/kept_rmvbyanno_maf
dropped_rmvbyanno_maf:
type: File[]
outputSource: module_4/dropped_rmvbyanno_maf
dropped_NGR_rmvbyanno_maf:
type: File[]
outputSource: module_4/dropped_NGR_rmvbyanno_maf
hotspots_filtered_maf:
type: File[]
outputSource: module_4/hotspots_filtered_maf
fillout_maf:
type: File[]
outputSource: module_4/fillout_maf
final_filtered_maf:
type: File[]
outputSource: module_4/final_filtered_maf
final_filtered_condensed_maf:
type: File[]
outputSource: module_4/final_filtered_condensed_maf
# collated_maf:
# type: File
# outputSource: module_5/collated_maf
#
# filtered_exonic:
# type: File
# outputSource: module_5/filtered_exonic
#
# dropped_exonic:
# type: File
# outputSource: module_5/dropped_exonic
#
# filtered_silent:
# type: File
# outputSource: module_5/filtered_silent
#
# dropped_silent:
# type: File
# outputSource: module_5/dropped_silent
#
# filtered_exonic_nonpanel:
# type: File
# outputSource: module_5/filtered_exonic_nonpanel
#
# dropped_exonic_nonpanel:
# type: File
# outputSource: module_5/dropped_exonic_nonpanel
#
# filtered_silent_nonpanel:
# type: File
# outputSource: module_5/filtered_silent_nonpanel
#
# dropped_silent_nonpanel:
# type: File
# outputSource: module_5/dropped_silent_nonpanel
#
# traceback_genotype_inputs:
# type: File
# outputSource: module_5/traceback_genotype_inputs
#
# tb_fillout_out:
# type: File
# outputSource: module_5/tb_fillout_out
#
# traceback_final:
# type: File
# outputSource: module_5/traceback_final
#
# tb_exonic_filtered_mutations:
# type: File
# outputSource: module_5/tb_exonic_filtered_mutations
#
# tb_exonic_dropped_mutations:
# type: File
# outputSource: module_5/tb_exonic_dropped_mutations
#
# tb_silent_filtered_mutations:
# type: File
# outputSource: module_5/tb_silent_filtered_mutations
#
# tb_silent_dropped_mutations:
# type: File
# outputSource: module_5/tb_silent_dropped_mutations
steps:
###################
# Variant Calling #
###################
module_3:
run: ../module-3.cwl
in:
run_tools: run_tools
tumor_bams: tumor_bams
normal_bams: normal_bams
tumor_sample_names: tumor_sample_names
normal_sample_names: normal_sample_names
bed_file: bed_file
ref_fasta: ref_fasta
dbsnp: dbsnp
cosmic: cosmic
mutect_params: mutect_params
vardict_params: vardict_params
basicfiltering_vardict_params: basicfiltering_vardict_params
basicfiltering_mutect_params: basicfiltering_mutect_params
bcftools_params: bcftools_params
annotate_concat_header_file: annotate_concat_header_file
out: [
concatenated_vcf,
annotated_concatenated_vcf,
mutect_vcf,
mutect_callstats,
vardict_vcf,
mutect_normalized_vcf,
vardict_normalized_vcf]
##############
# Genotyping #
##############
module_4:
run: ../module-4.cwl
in:
run_tools: run_tools
vcf2maf_params: vcf2maf_params
access_filters_params: access_filters_params
hotspots: hotspots
blacklist_file: blacklist_file
custom_enst_file: custom_enst_file
gbcms_params: gbcms_params
combine_vcf: module_3/annotated_concatenated_vcf
genotyping_bams: genotyping_bams
genotyping_bams_ids: genotyping_bams_ids
tumor_sample_name: tumor_sample_names
normal_sample_name: normal_sample_names
matched_normal_sample_name: matched_normal_ids
ref_fasta: ref_fasta
exac_filter: exac_filter
out: [
maf,
kept_rmvbyanno_maf,
dropped_rmvbyanno_maf,
dropped_NGR_rmvbyanno_maf,
hotspots_filtered_maf,
fillout_maf,
final_filtered_maf,
final_filtered_condensed_maf]
scatter: [combine_vcf, tumor_sample_name, normal_sample_name, matched_normal_sample_name]
scatterMethod: dotproduct
####################################
# Convert maf to tsv and traceback #
####################################
# module_5:
# run: ../module-5.cwl
# in:
# project_name: project_name
# custom_enst_file: custom_enst_file
# all_maf: module_4/final_filtered_maf
# title_file: title_file
# gbcms_params: gbcms_params
# run_tools: run_tools
# traceback_sample_ids: traceback_sample_ids
# traceback_bams: traceback_bams
# traceback_input_mutations: traceback_mutation_file
# ref_fasta: ref_fasta
# out: [
# collated_maf,
# filtered_exonic,
# dropped_exonic,
# filtered_silent,
# dropped_silent,
# filtered_exonic_nonpanel,
# dropped_exonic_nonpanel,
# filtered_silent_nonpanel,
# dropped_silent_nonpanel,
# traceback_genotype_inputs,
# tb_fillout_out,
# traceback_final,
# tb_exonic_filtered_mutations,
# tb_exonic_dropped_mutations,
# tb_silent_filtered_mutations,
# tb_silent_dropped_mutations]