#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow requirements: - class: InlineJavascriptRequirement - class: StepInputExpressionRequirement - class: SubworkflowFeatureRequirement inputs: - id: bioclient_config type: File - id: bioclient_load_bucket type: string - 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: 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: slurm_resource_cores type: long - id: slurm_resource_disk_gigabytes type: long - id: slurm_resource_mem_megabytes type: long - id: status_table type: string - id: job_uuid type: string - 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_mirna_profiling_tar_uuid type: string outputSource: emit_mirna_profiling_tar_uuid/output - id: indexd_mirna_profiling_isoforms_quant_uuid type: string outputSource: emit_mirna_profiling_isoforms_quant_uuid/output - id: indexd_mirna_profiling_mirnas_quant_uuid type: string outputSource: emit_mirna_profiling_mirnas_quant_uuid/output - id: indexd_sqlite_uuid type: string outputSource: emit_sqlite_uuid/output steps: - id: get_hostname run: ../../tools/emit_hostname.cwl in: [] out: - id: output - id: get_host_ipaddress run: ../../tools/emit_host_ipaddress.cwl in: [] out: - id: output - id: get_host_macaddress run: ../../tools/emit_host_mac.cwl in: [] out: - id: output - id: status_running run: status_postgres.cwl in: - id: cwl_workflow_git_hash source: cwl_workflow_git_hash - id: cwl_workflow_git_repo source: cwl_workflow_git_repo - id: cwl_workflow_rel_path source: cwl_workflow_rel_path - id: cwl_job_git_hash source: cwl_job_git_hash - id: cwl_job_git_repo source: cwl_job_git_repo - id: cwl_job_rel_path source: cwl_job_rel_path - id: db_cred source: db_cred - id: db_cred_section source: db_cred_section - id: hostname source: get_hostname/output - id: host_ipaddress source: get_host_ipaddress/output - id: host_macaddress source: get_host_macaddress/output - id: input_bam_gdc_id source: input_bam_gdc_id - id: input_bam_file_size source: input_bam_file_size - id: input_bam_md5sum source: input_bam_md5sum - id: known_snp_gdc_id source: known_snp_gdc_id - id: known_snp_file_size source: known_snp_file_size - id: known_snp_index_gdc_id source: known_snp_index_gdc_id - id: known_snp_index_file_size source: known_snp_index_file_size - id: reference_amb_gdc_id source: reference_amb_gdc_id - id: reference_amb_file_size source: reference_amb_file_size - id: reference_ann_gdc_id source: reference_ann_gdc_id - id: reference_ann_file_size source: reference_ann_file_size - id: reference_bwt_gdc_id source: reference_bwt_gdc_id - id: reference_bwt_file_size source: reference_bwt_file_size - id: reference_dict_gdc_id source: reference_dict_gdc_id - id: reference_dict_file_size source: reference_dict_file_size - id: reference_fa_gdc_id source: reference_fa_gdc_id - id: reference_fa_file_size source: reference_fa_file_size - id: reference_fai_gdc_id source: reference_fai_gdc_id - id: reference_fai_file_size source: reference_fai_file_size - id: reference_pac_gdc_id source: reference_pac_gdc_id - id: reference_pac_file_size source: reference_pac_file_size - id: reference_sa_gdc_id source: reference_sa_gdc_id - id: reference_sa_file_size source: reference_sa_file_size - id: indexd_bam_uuid valueFrom: "NULL" - id: indexd_bai_uuid valueFrom: "NULL" - id: indexd_mirna_profiling_tar_uuid valueFrom: "NULL" - id: indexd_mirna_profiling_isoforms_quant_uuid valueFrom: "NULL" - id: indexd_mirna_profiling_mirnas_quant_uuid valueFrom: "NULL" - id: indexd_sqlite_uuid valueFrom: "NULL" - id: slurm_resource_cores source: slurm_resource_cores - id: slurm_resource_disk_gigabytes source: slurm_resource_disk_gigabytes - id: slurm_resource_mem_megabytes source: slurm_resource_mem_megabytes - id: status valueFrom: "RUNNING" - id: step_token source: bioclient_config - id: table_name source: status_table - id: job_uuid source: job_uuid - id: thread_count source: thread_count out: - id: token - id: etl run: etl.cwl in: - id: bioclient_config source: bioclient_config - id: bioclient_load_bucket source: bioclient_load_bucket - id: input_bam_gdc_id source: input_bam_gdc_id - id: input_bam_file_size source: input_bam_file_size - id: known_snp_gdc_id source: known_snp_gdc_id - id: known_snp_file_size source: known_snp_file_size - id: known_snp_index_gdc_id source: known_snp_index_gdc_id - id: known_snp_index_file_size source: known_snp_index_file_size - id: reference_amb_gdc_id source: reference_amb_gdc_id - id: reference_amb_file_size source: reference_amb_file_size - id: reference_ann_gdc_id source: reference_ann_gdc_id - id: reference_ann_file_size source: reference_ann_file_size - id: reference_bwt_gdc_id source: reference_bwt_gdc_id - id: reference_bwt_file_size source: reference_bwt_file_size - id: reference_dict_gdc_id source: reference_dict_gdc_id - id: reference_dict_file_size source: reference_dict_file_size - id: reference_fa_gdc_id source: reference_fa_gdc_id - id: reference_fa_file_size source: reference_fa_file_size - id: reference_fai_gdc_id source: reference_fai_gdc_id - id: reference_fai_file_size source: reference_fai_file_size - id: reference_pac_gdc_id source: reference_pac_gdc_id - id: reference_pac_file_size source: reference_pac_file_size - id: reference_sa_gdc_id source: reference_sa_gdc_id - id: reference_sa_file_size source: reference_sa_file_size - id: start_token source: status_running/token - id: thread_count source: thread_count - id: job_uuid source: job_uuid out: - id: indexd_bam_json - id: indexd_bai_json - id: indexd_mirna_profiling_tar_json - id: indexd_mirna_profiling_isoforms_quant_json - id: indexd_mirna_profiling_mirnas_quant_json - id: indexd_sqlite_json - id: token - id: emit_bam_uuid run: ../../tools/emit_json_value.cwl in: - id: input source: etl/indexd_bam_json - id: key valueFrom: did out: - id: output - id: emit_bai_uuid run: ../../tools/emit_json_value.cwl in: - id: input source: etl/indexd_bai_json - id: key valueFrom: did out: - id: output - id: emit_sqlite_uuid run: ../../tools/emit_json_value.cwl in: - id: input source: etl/indexd_sqlite_json - id: key valueFrom: did out: - id: output - id: emit_mirna_profiling_tar_uuid run: ../../tools/emit_json_value.cwl in: - id: input source: etl/indexd_mirna_profiling_tar_json - id: key valueFrom: did out: - id: output - id: emit_mirna_profiling_isoforms_quant_uuid run: ../../tools/emit_json_value.cwl in: - id: input source: etl/indexd_mirna_profiling_isoforms_quant_json - id: key valueFrom: did out: - id: output - id: emit_mirna_profiling_mirnas_quant_uuid run: ../../tools/emit_json_value.cwl in: - id: input source: etl/indexd_mirna_profiling_mirnas_quant_json - id: key valueFrom: did out: - id: output - id: status_complete run: status_postgres.cwl in: - id: cwl_workflow_git_hash source: cwl_workflow_git_hash - id: cwl_workflow_git_repo source: cwl_workflow_git_repo - id: cwl_workflow_rel_path source: cwl_workflow_rel_path - id: cwl_job_git_hash source: cwl_job_git_hash - id: cwl_job_git_repo source: cwl_job_git_repo - id: cwl_job_rel_path source: cwl_job_rel_path - id: db_cred source: db_cred - id: db_cred_section source: db_cred_section - id: hostname source: get_hostname/output - id: host_ipaddress source: get_host_ipaddress/output - id: host_macaddress source: get_host_macaddress/output - id: input_bam_gdc_id source: input_bam_gdc_id - id: input_bam_file_size source: input_bam_file_size - id: input_bam_md5sum source: input_bam_md5sum - id: known_snp_gdc_id source: known_snp_gdc_id - id: known_snp_file_size source: known_snp_file_size - id: known_snp_index_gdc_id source: known_snp_index_gdc_id - id: known_snp_index_file_size source: known_snp_index_file_size - id: reference_amb_gdc_id source: reference_amb_gdc_id - id: reference_amb_file_size source: reference_amb_file_size - id: reference_ann_gdc_id source: reference_ann_gdc_id - id: reference_ann_file_size source: reference_ann_file_size - id: reference_bwt_gdc_id source: reference_bwt_gdc_id - id: reference_bwt_file_size source: reference_bwt_file_size - id: reference_dict_gdc_id source: reference_dict_gdc_id - id: reference_dict_file_size source: reference_dict_file_size - id: reference_fa_gdc_id source: reference_fa_gdc_id - id: reference_fa_file_size source: reference_fa_file_size - id: reference_fai_gdc_id source: reference_fai_gdc_id - id: reference_fai_file_size source: reference_fai_file_size - id: reference_pac_gdc_id source: reference_pac_gdc_id - id: reference_pac_file_size source: reference_pac_file_size - id: reference_sa_gdc_id source: reference_sa_gdc_id - id: reference_sa_file_size source: reference_sa_file_size - id: indexd_bam_uuid source: emit_bam_uuid/output - id: indexd_bai_uuid source: emit_bai_uuid/output - id: indexd_mirna_profiling_tar_uuid source: emit_mirna_profiling_tar_uuid/output - id: indexd_mirna_profiling_isoforms_quant_uuid source: emit_mirna_profiling_isoforms_quant_uuid/output - id: indexd_mirna_profiling_mirnas_quant_uuid source: emit_mirna_profiling_mirnas_quant_uuid/output - id: indexd_sqlite_uuid source: emit_sqlite_uuid/output - id: slurm_resource_cores source: slurm_resource_cores - id: slurm_resource_disk_gigabytes source: slurm_resource_disk_gigabytes - id: slurm_resource_mem_megabytes source: slurm_resource_mem_megabytes - id: status valueFrom: "COMPLETE" - id: step_token source: etl/token - id: table_name source: status_table - id: job_uuid source: job_uuid - id: thread_count source: thread_count out: - id: token