/
etl.cwl
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/
etl.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- 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: bioclient_config
type: File
- id: bioclient_load_bucket
type: string
- id: job_uuid
type: string
- id: amplicon_kit_set_uuid_list
type:
type: array
items: ../../tools/amplicon_kit.yml#amplicon_kit_set_uuid
- id: capture_kit_set_uuid_list
type:
type: array
items: ../../tools/capture_kit.yml#capture_kit_set_uuid
- id: readgroup_fastq_pe_uuid_list
type:
type: array
items: ../../tools/readgroup.yml#readgroup_fastq_pe_uuid
- id: readgroup_fastq_se_uuid_list
type:
type: array
items: ../../tools/readgroup.yml#readgroup_fastq_se_uuid
- id: readgroups_bam_uuid_list
type:
type: array
items: ../../tools/readgroup.yml#readgroups_bam_uuid
- id: start_token
type: ["null", File]
- id: known_snp_gdc_id
type: string
- id: known_snp_file_size
type: long
- id: known_snp_index_gdc_id
type: string
- id: known_snp_index_file_size
type: long
- id: reference_amb_gdc_id
type: string
- id: reference_amb_file_size
type: long
- id: reference_ann_gdc_id
type: string
- id: reference_ann_file_size
type: long
- id: reference_bwt_gdc_id
type: string
- id: reference_bwt_file_size
type: long
- id: reference_dict_gdc_id
type: string
- id: reference_dict_file_size
type: long
- id: reference_fa_gdc_id
type: string
- id: reference_fa_file_size
type: long
- id: reference_fai_gdc_id
type: string
- id: reference_fai_file_size
type: long
- id: reference_pac_gdc_id
type: string
- id: reference_pac_file_size
type: long
- id: reference_sa_gdc_id
type: string
- id: reference_sa_file_size
type: long
- id: run_bamindex
type:
type: array
items: long
- id: run_markduplicates
type:
type: array
items: long
- id: thread_count
type: long
outputs:
- id: indexd_bam_uuid
type: string
outputSource: emit_bam_uuid/output
- id: indexd_bai_uuid
type: string
outputSource: emit_bai_uuid/output
- id: indexd_sqlite_uuid
type: string
outputSource: emit_sqlite_uuid/output
steps:
- id: extract_readgroup_fastq_pe
run: extract_readgroup_fastq_pe.cwl
scatter: readgroup_fastq_pe_uuid
in:
- id: readgroup_fastq_pe_uuid
source: readgroup_fastq_pe_uuid_list
- id: bioclient_config
source: bioclient_config
out:
- id: output
- id: extract_readgroup_fastq_se
run: extract_readgroup_fastq_se.cwl
scatter: readgroup_fastq_se_uuid
in:
- id: readgroup_fastq_se_uuid
source: readgroup_fastq_se_uuid_list
- id: bioclient_config
source: bioclient_config
out:
- id: output
- id: extract_readgroups_bam
run: extract_readgroups_bam.cwl
scatter: [readgroups_bam_uuid]
in:
- id: readgroups_bam_uuid
source: readgroups_bam_uuid_list
- id: bioclient_config
source: bioclient_config
out:
- id: output
- id: extract_amplicon_kits
run: extract_amplicon_kit.cwl
scatter: amplicon_kit_set_uuid
in:
- id: bioclient_config
source: bioclient_config
- id: amplicon_kit_set_uuid
source: amplicon_kit_set_uuid_list
out:
- id: output
- id: extract_capture_kits
run: extract_capture_kit.cwl
scatter: capture_kit_set_uuid
in:
- id: bioclient_config
source: bioclient_config
- id: capture_kit_set_uuid
source: capture_kit_set_uuid_list
out:
- id: output
- id: extract_known_snp
run: ../../tools/bio_client_download.cwl
in:
- id: config-file
source: bioclient_config
- id: download_handle
source: known_snp_gdc_id
- id: file_size
source: known_snp_file_size
out:
- id: output
- id: extract_known_snp_index
run: ../../tools/bio_client_download.cwl
in:
- id: config-file
source: bioclient_config
- id: download_handle
source: known_snp_index_gdc_id
- id: file_size
source: known_snp_index_file_size
out:
- id: output
- id: extract_reference_amb
run: ../../tools/bio_client_download.cwl
in:
- id: config-file
source: bioclient_config
- id: download_handle
source: reference_amb_gdc_id
- id: file_size
source: reference_amb_file_size
out:
- id: output
- id: extract_reference_ann
run: ../../tools/bio_client_download.cwl
in:
- id: config-file
source: bioclient_config
- id: download_handle
source: reference_ann_gdc_id
- id: file_size
source: reference_ann_file_size
out:
- id: output
- id: extract_reference_bwt
run: ../../tools/bio_client_download.cwl
in:
- id: config-file
source: bioclient_config
- id: download_handle
source: reference_bwt_gdc_id
- id: file_size
source: reference_bwt_file_size
out:
- id: output
- id: extract_reference_dict
run: ../../tools/bio_client_download.cwl
in:
- id: config-file
source: bioclient_config
- id: download_handle
source: reference_dict_gdc_id
- id: file_size
source: reference_dict_file_size
out:
- id: output
- id: extract_reference_fa
run: ../../tools/bio_client_download.cwl
in:
- id: config-file
source: bioclient_config
- id: download_handle
source: reference_fa_gdc_id
- id: file_size
source: reference_fa_file_size
out:
- id: output
- id: extract_reference_fai
run: ../../tools/bio_client_download.cwl
in:
- id: config-file
source: bioclient_config
- id: download_handle
source: reference_fai_gdc_id
- id: file_size
source: reference_fai_file_size
out:
- id: output
- id: extract_reference_pac
run: ../../tools/bio_client_download.cwl
in:
- id: config-file
source: bioclient_config
- id: download_handle
source: reference_pac_gdc_id
- id: file_size
source: reference_pac_file_size
out:
- id: output
- id: extract_reference_sa
run: ../../tools/bio_client_download.cwl
in:
- id: config-file
source: bioclient_config
- id: download_handle
source: reference_sa_gdc_id
- id: file_size
source: reference_sa_file_size
out:
- id: output
- id: root_fasta_files
run: ../../tools/root_fasta_dnaseq.cwl
in:
- id: fasta
source: extract_reference_fa/output
- id: fasta_amb
source: extract_reference_amb/output
- id: fasta_ann
source: extract_reference_ann/output
- id: fasta_bwt
source: extract_reference_bwt/output
- id: fasta_dict
source: extract_reference_dict/output
- id: fasta_fai
source: extract_reference_fai/output
- id: fasta_pac
source: extract_reference_pac/output
- id: fasta_sa
source: extract_reference_sa/output
out:
- id: output
- id: root_known_snp_files
run: ../../tools/root_vcf.cwl
in:
- id: vcf
source: extract_known_snp/output
- id: vcf_index
source: extract_known_snp_index/output
out:
- id: output
- id: transform
run: transform.cwl
in:
- id: bam_name
source: bam_name
- id: job_uuid
source: job_uuid
- id: amplicon_kit_set_file_list
source: extract_amplicon_kits/output
- id: capture_kit_set_file_list
source: extract_capture_kits/output
- id: readgroup_fastq_pe_file_list
source: extract_readgroup_fastq_pe/output
- id: readgroup_fastq_se_file_list
source: extract_readgroup_fastq_se/output
- id: readgroups_bam_file_list
source: extract_readgroups_bam/output
- id: known_snp
source: root_known_snp_files/output
- id: reference_sequence
source: root_fasta_files/output
- id: run_bamindex
source: run_bamindex
- id: run_markduplicates
source: run_markduplicates
- id: thread_count
source: thread_count
out:
- id: output_bam
- id: sqlite
- id: load_bam
run: ../../tools/bio_client_upload_pull_uuid.cwl
in:
- id: config-file
source: bioclient_config
- id: input
source: transform/output_bam
- id: upload-bucket
source: bioclient_load_bucket
- id: upload-key
valueFrom: $(inputs.job_uuid)/$(inputs.input.basename)
- id: job_uuid
source: job_uuid
valueFrom: $(null)
out:
- id: output
- id: load_bai
run: ../../tools/bio_client_upload_pull_uuid.cwl
in:
- id: config-file
source: bioclient_config
- id: input
source: transform/output_bam
valueFrom: $(self.secondaryFiles[0])
- id: upload-bucket
source: bioclient_load_bucket
- id: upload-key
valueFrom: $(inputs.job_uuid)/$(inputs.input.nameroot).bai
- id: job_uuid
source: job_uuid
valueFrom: $(null)
out:
- id: output
- id: load_sqlite
run: ../../tools/bio_client_upload_pull_uuid.cwl
in:
- id: config-file
source: bioclient_config
- id: input
source: transform/sqlite
- id: upload-bucket
source: bioclient_load_bucket
- id: upload-key
valueFrom: $(inputs.job_uuid)/$(inputs.input.basename)
- id: job_uuid
source: job_uuid
valueFrom: $(null)
out:
- id: output
- id: emit_bam_uuid
run: ../../tools/emit_json_value.cwl
in:
- id: input
source: load_bam/output
- id: key
valueFrom: did
out:
- id: output
- id: emit_bai_uuid
run: ../../tools/emit_json_value.cwl
in:
- id: input
source: load_bai/output
- id: key
valueFrom: did
out:
- id: output
- id: emit_sqlite_uuid
run: ../../tools/emit_json_value.cwl
in:
- id: input
source: load_sqlite/output
- id: key
valueFrom: did
out:
- id: output