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status_postgres.cwl
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status_postgres.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- class: MultipleInputFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
- id: cwl_workflow_git_hash
type: string
- id: cwl_workflow_git_repo
type: string
- id: cwl_workflow_rel_path
type: string
- id: cwl_job_git_hash
type: string
- id: cwl_job_git_repo
type: string
- id: cwl_job_rel_path
type: string
- id: db_cred
type: File
- id: db_cred_section
type: string
- id: hostname
type: string
- id: host_ipaddress
type: string
- id: host_macaddress
type: string
- id: input_bam_gdc_id
type: string
- id: input_bam_file_size
type: long
- id: input_bam_md5sum
type: string
- 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: indexd_bam_uuid
type: string
- id: indexd_bai_uuid
type: string
- id: indexd_mirna_profiling_tar_uuid
type: string
- id: indexd_mirna_profiling_isoforms_quant_uuid
type: string
- id: indexd_mirna_profiling_mirnas_quant_uuid
type: string
- id: indexd_sqlite_uuid
type: string
- id: slurm_resource_cores
type: long
- id: slurm_resource_disk_gigabytes
type: long
- id: slurm_resource_mem_megabytes
type: long
- id: status
type: string
- id: step_token
type: File
- id: table_name
type: string
- id: job_uuid
type: string
- id: thread_count
type: long
outputs:
- id: token
type: File
outputSource: sqlite_to_postgres/log
steps:
- id: emit_json
run: ../../tools/emit_json.cwl
in:
- id: string_keys
default: [
"cwl_workflow_git_hash",
"cwl_workflow_git_repo",
"cwl_workflow_rel_path",
"cwl_job_git_hash",
"cwl_job_git_repo",
"cwl_job_rel_path",
"hostname",
"host_ipaddress",
"host_macaddress",
"input_bam_gdc_id",
"input_bam_md5sum",
"known_snp_gdc_id",
"known_snp_index_gdc_id",
"reference_amb_gdc_id",
"reference_ann_gdc_id",
"reference_bwt_gdc_id",
"reference_dict_gdc_id",
"reference_fa_gdc_id",
"reference_fai_gdc_id",
"reference_pac_gdc_id",
"reference_sa_gdc_id",
"indexd_bam_uuid",
"indexd_bai_uuid",
"indexd_mirna_profiling_tar_uuid",
"indexd_mirna_profiling_isoforms_quant_uuid",
"indexd_mirna_profiling_mirnas_quant_uuid",
"indexd_sqlite_uuid",
"status",
"job_uuid"
]
- id: string_values
source: [
cwl_workflow_git_hash,
cwl_workflow_git_repo,
cwl_workflow_rel_path,
cwl_job_git_hash,
cwl_job_git_repo,
cwl_job_rel_path,
hostname,
host_ipaddress,
host_macaddress,
input_bam_gdc_id,
input_bam_md5sum,
known_snp_gdc_id,
known_snp_index_gdc_id,
reference_amb_gdc_id,
reference_ann_gdc_id,
reference_bwt_gdc_id,
reference_dict_gdc_id,
reference_fa_gdc_id,
reference_fai_gdc_id,
reference_pac_gdc_id,
reference_sa_gdc_id,
indexd_bam_uuid,
indexd_bai_uuid,
indexd_mirna_profiling_tar_uuid,
indexd_mirna_profiling_isoforms_quant_uuid,
indexd_mirna_profiling_mirnas_quant_uuid,
indexd_sqlite_uuid,
status,
job_uuid
]
- id: long_keys
default: [
"input_bam_file_size",
"known_snp_file_size",
"known_snp_index_file_size",
"reference_amb_file_size",
"reference_ann_file_size",
"reference_bwt_file_size",
"reference_dict_file_size",
"reference_fa_file_size",
"reference_fai_file_size",
"reference_pac_file_size",
"reference_sa_file_size",
"slurm_resource_cores",
"slurm_resource_disk_gigabytes",
"slurm_resource_mem_megabytes",
"thread_count"
]
- id: long_values
source: [
input_bam_file_size,
known_snp_file_size,
known_snp_index_file_size,
reference_amb_file_size,
reference_ann_file_size,
reference_bwt_file_size,
reference_dict_file_size,
reference_fa_file_size,
reference_fai_file_size,
reference_pac_file_size,
reference_sa_file_size,
slurm_resource_cores,
slurm_resource_disk_gigabytes,
slurm_resource_mem_megabytes,
thread_count
]
- id: float_keys
default: []
- id: float_values
default: []
out:
- id: output
- id: json_to_sqlite
run: ../../tools/json_to_sqlite.cwl
in:
- id: input_json
source: emit_json/output
- id: job_uuid
source: job_uuid
- id: table_name
source: table_name
out:
- id: sqlite
- id: log
- id: sqlite_to_postgres
run: ../../tools/sqlite_to_postgres_hirate.cwl
in:
- id: postgres_creds_path
source: db_cred
- id: ini_section
source: db_cred_section
- id: source_sqlite_path
source: json_to_sqlite/sqlite
- id: job_uuid
source: job_uuid
out:
- id: log