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integrity.cwl
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integrity.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: StepInputExpressionRequirement
- class: MultipleInputFeatureRequirement
inputs:
- id: bai
type: File
- id: bam
type: File
- id: input_state
type: string
- id: job_uuid
type: string
outputs:
- id: merge_sqlite_destination_sqlite
type: File
outputSource: merge_sqlite/destination_sqlite
steps:
- id: bai_ls_l
run: ../../tools/ls_l.cwl
in:
- id: INPUT
source: bai
out:
- id: OUTPUT
- id: bai_md5sum
run: ../../tools/md5sum.cwl
in:
- id: INPUT
source: bai
out:
- id: OUTPUT
- id: bai_sha256
run: ../../tools/sha256sum.cwl
in:
- id: INPUT
source: bai
out:
- id: OUTPUT
- id: bam_ls_l
run: ../../tools/ls_l.cwl
in:
- id: INPUT
source: bam
out:
- id: OUTPUT
- id: bam_md5sum
run: ../../tools/md5sum.cwl
in:
- id: INPUT
source: bam
out:
- id: OUTPUT
- id: bam_sha256
run: ../../tools/sha256sum.cwl
in:
- id: INPUT
source: bam
out:
- id: OUTPUT
- id: bai_integrity_to_db
run: ../../tools/integrity_to_sqlite.cwl
in:
- id: input_state
source: input_state
- id: ls_l_path
source: bai_ls_l/OUTPUT
- id: md5sum_path
source: bai_md5sum/OUTPUT
- id: sha256sum_path
source: bai_sha256/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: OUTPUT
- id: bam_integrity_to_db
run: ../../tools/integrity_to_sqlite.cwl
in:
- id: input_state
source: input_state
- id: ls_l_path
source: bam_ls_l/OUTPUT
- id: md5sum_path
source: bam_md5sum/OUTPUT
- id: sha256sum_path
source: bam_sha256/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: OUTPUT
- id: merge_sqlite
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: [
bai_integrity_to_db/OUTPUT,
bam_integrity_to_db/OUTPUT
]
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log