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transform.cwl
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transform.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- class: MultipleInputFeatureRequirement
- class: ScatterFeatureRequirement
- class: SchemaDefRequirement
types:
- $import: ../../tools/amplicon_kit.yml
- $import: ../../tools/capture_kit.yml
- $import: ../../tools/readgroup.yml
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
inputs:
- id: bam_name
type: string
- id: job_uuid
type: string
- id: amplicon_kit_set_file_list
type:
type: array
items: ../../tools/amplicon_kit.yml#amplicon_kit_set_file
- id: capture_kit_set_file_list
type:
type: array
items: ../../tools/capture_kit.yml#capture_kit_set_file
- id: readgroup_fastq_pe_file_list
type:
type: array
items: ../../tools/readgroup.yml#readgroup_fastq_pe_file
- id: readgroup_fastq_se_file_list
type:
type: array
items: ../../tools/readgroup.yml#readgroup_fastq_se_file
- id: readgroups_bam_file_list
type:
type: array
items: ../../tools/readgroup.yml#readgroups_bam_file
- id: common_biallelic_vcf
type: File
secondaryFiles:
- .tbi
- id: known_snp
type: File
secondaryFiles:
- .tbi
- id: run_bamindex
type:
type: array
items: long
- id: run_markduplicates
type:
type: array
items: long
- id: reference_sequence
type: File
secondaryFiles:
- .amb
- .ann
- .bwt
- .fai
- .pac
- .sa
- ^.dict
- id: thread_count
type: long
outputs:
- id: output_bam
type: File
outputSource: gatk_applybqsr/output_bam
- id: sqlite
type: File
outputSource: merge_all_sqlite/destination_sqlite
steps:
- id: fastq_clean_pe
run: fastq_clean_pe.cwl
scatter: input
in:
- id: input
source: readgroup_fastq_pe_file_list
- id: job_uuid
source: job_uuid
out:
- id: output
- id: sqlite
- id: fastq_clean_se
run: fastq_clean_se.cwl
scatter: input
in:
- id: input
source: readgroup_fastq_se_file_list
- id: job_uuid
source: job_uuid
out:
- id: output
- id: sqlite
- id: merge_sqlite_fastq_clean_pe
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: fastq_clean_pe/sqlite
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log
- id: merge_sqlite_fastq_clean_se
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: fastq_clean_se/sqlite
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log
- id: readgroups_bam_to_readgroups_fastq_lists
run: readgroups_bam_to_readgroups_fastq_lists.cwl
scatter: readgroups_bam_file
in:
- id: readgroups_bam_file
source: readgroups_bam_file_list
out:
- id: pe_file_list
- id: se_file_list
- id: o1_file_list
- id: o2_file_list
- id: merge_bam_pe_fastq_records
run: ../../tools/merge_pe_fastq_records.cwl
in:
- id: input
source: readgroups_bam_to_readgroups_fastq_lists/pe_file_list
out:
- id: output
- id: merge_pe_fastq_records
run: ../../tools/merge_pe_fastq_records.cwl
in:
- id: input
source: [
merge_bam_pe_fastq_records/output,
fastq_clean_pe/output
]
out:
- id: output
- id: merge_bam_se_fastq_records
run: ../../tools/merge_se_fastq_records.cwl
in:
- id: input
source: readgroups_bam_to_readgroups_fastq_lists/se_file_list
out:
- id: output
- id: merge_se_fastq_records
run: ../../tools/merge_se_fastq_records.cwl
in:
- id: input
source: [
merge_bam_se_fastq_records/output,
fastq_clean_se/output
]
out:
- id: output
- id: merge_o1_fastq_records
run: ../../tools/merge_se_fastq_records.cwl
in:
- id: input
source: readgroups_bam_to_readgroups_fastq_lists/o1_file_list
out:
- id: output
- id: merge_o2_fastq_records
run: ../../tools/merge_se_fastq_records.cwl
in:
- id: input
source: readgroups_bam_to_readgroups_fastq_lists/o2_file_list
out:
- id: output
- id: bwa_pe
run: bwa_pe.cwl
scatter: readgroup_fastq_pe
in:
- id: job_uuid
source: job_uuid
- id: reference_sequence
source: reference_sequence
- id: readgroup_fastq_pe
source: merge_pe_fastq_records/output
- id: thread_count
source: thread_count
out:
- id: bam
- id: sqlite
- id: bwa_se
run: bwa_se.cwl
scatter: readgroup_fastq_se
in:
- id: job_uuid
source: job_uuid
- id: reference_sequence
source: reference_sequence
- id: readgroup_fastq_se
source: merge_se_fastq_records/output
- id: thread_count
source: thread_count
out:
- id: bam
- id: sqlite
- id: bwa_o1
run: bwa_se.cwl
scatter: readgroup_fastq_se
in:
- id: job_uuid
source: job_uuid
- id: reference_sequence
source: reference_sequence
- id: readgroup_fastq_se
source: merge_o1_fastq_records/output
- id: thread_count
source: thread_count
out:
- id: bam
- id: sqlite
- id: bwa_o2
run: bwa_se.cwl
scatter: readgroup_fastq_se
in:
- id: job_uuid
source: job_uuid
- id: reference_sequence
source: reference_sequence
- id: readgroup_fastq_se
source: merge_o2_fastq_records/output
- id: thread_count
source: thread_count
out:
- id: bam
- id: sqlite
- id: merge_sqlite_bwa_pe
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: bwa_pe/sqlite
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log
- id: merge_sqlite_bwa_se
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: bwa_se/sqlite
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log
- id: picard_mergesamfiles
run: ../../tools/picard_mergesamfiles_aoa.cwl
in:
- id: INPUT
source: [
bwa_pe/bam,
bwa_se/bam,
bwa_o1/bam,
bwa_o2/bam
]
- id: OUTPUT
source: bam_name
out:
- id: MERGED_OUTPUT
- id: bam_reheader
run: ../../tools/bam_reheader.cwl
in:
- id: input
source: picard_mergesamfiles/MERGED_OUTPUT
out:
- id: output
- id: conditional_markduplicates
run: conditional_markduplicates.cwl
scatter: run_markduplicates
in:
- id: bam
source: bam_reheader/output
- id: job_uuid
source: job_uuid
- id: run_markduplicates
source: run_markduplicates
out:
- id: output
- id: sqlite
- id: conditional_index
run: conditional_bamindex.cwl
scatter: run_bamindex
in:
- id: bam
source: bam_reheader/output
- id: run_bamindex
source: run_bamindex
- id: thread_count
source: thread_count
out:
- id: output
- id: sqlite
- id: decide_markduplicates_index
run: ../../tools/decider_conditional_bams.cwl
in:
- id: conditional_bam1
source: conditional_markduplicates/output
- id: conditional_sqlite1
source: conditional_markduplicates/sqlite
- id: conditional_bam2
source: conditional_index/output
- id: conditional_sqlite2
source: conditional_index/sqlite
out:
- id: output
- id: sqlite
- id: gatk_baserecalibrator
run: ../../tools/gatk4_baserecalibrator.cwl
in:
- id: input
source: decide_markduplicates_index/output
- id: known-sites
source: known_snp
- id: reference
source: reference_sequence
out:
- id: output_grp
- id: gatk_applybqsr
run: ../../tools/gatk4_applybqsr.cwl
in:
- id: input
source: decide_markduplicates_index/output
- id: bqsr-recal-file
source: gatk_baserecalibrator/output_grp
out:
- id: output_bam
- id: picard_validatesamfile_bqsr
run: ../../tools/picard_validatesamfile.cwl
in:
- id: INPUT
source: gatk_applybqsr/output_bam
- id: VALIDATION_STRINGENCY
valueFrom: "STRICT"
out:
- id: OUTPUT
#need eof and dup QNAME detection
- id: picard_validatesamfile_bqsr_to_sqlite
run: ../../tools/picard_validatesamfile_to_sqlite.cwl
in:
- id: bam
source: gatk_applybqsr/output_bam
valueFrom: $(self.basename)
- id: input_state
valueFrom: "gatk_applybqsr_readgroups"
- id: metric_path
source: picard_validatesamfile_bqsr/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: sqlite
- id: metrics
run: metrics.cwl
in:
- id: bam
source: gatk_applybqsr/output_bam
- id: amplicon_kit_set_file_list
source: amplicon_kit_set_file_list
- id: capture_kit_set_file_list
source: capture_kit_set_file_list
- id: common_biallelic_vcf
source: common_biallelic_vcf
- id: fasta
source: reference_sequence
- id: input_state
valueFrom: "gatk_applybqsr_readgroups"
- id: job_uuid
source: job_uuid
- id: known_snp
source: known_snp
out:
- id: sqlite
- id: integrity
run: integrity.cwl
in:
- id: bai
source: gatk_applybqsr/output_bam
valueFrom: $(self.secondaryFiles[0])
- id: bam
source: gatk_applybqsr/output_bam
- id: input_state
valueFrom: "gatk_applybqsr_readgroups"
- id: job_uuid
source: job_uuid
out:
- id: sqlite
- id: merge_all_sqlite
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: [
merge_sqlite_fastq_clean_pe/destination_sqlite,
merge_sqlite_fastq_clean_se/destination_sqlite,
merge_sqlite_bwa_pe/destination_sqlite,
merge_sqlite_bwa_se/destination_sqlite,
decide_markduplicates_index/sqlite,
picard_validatesamfile_bqsr_to_sqlite/sqlite,
metrics/sqlite,
integrity/sqlite
]
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log