CWL Workflow: runner.cwl

This workflow is Open Source and may be reused according to the terms of: Apache License 2.0

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
db_cred	File
job_uuid	String
status_table	String
thread_count	Long
db_cred_section	String
bioclient_config	File
cwl_job_git_hash	String
cwl_job_git_repo	String
cwl_job_rel_path	String
input_bam_gdc_id	String
input_bam_md5sum	String
known_snp_gdc_id	String
input_bam_file_size	Long
known_snp_file_size	Long
reference_fa_gdc_id	String
reference_sa_gdc_id	String
reference_amb_gdc_id	String
reference_ann_gdc_id	String
reference_bwt_gdc_id	String
reference_fai_gdc_id	String
reference_pac_gdc_id	String
slurm_resource_cores	Long
bioclient_load_bucket	String
cwl_workflow_git_hash	String
cwl_workflow_git_repo	String
cwl_workflow_rel_path	String
reference_dict_gdc_id	String
known_snp_index_gdc_id	String
reference_fa_file_size	Long
reference_sa_file_size	Long
reference_amb_file_size	Long
reference_ann_file_size	Long
reference_bwt_file_size	Long
reference_fai_file_size	Long
reference_pac_file_size	Long
reference_dict_file_size	Long
known_snp_index_file_size	Long
slurm_resource_mem_megabytes	Long
slurm_resource_disk_gigabytes	Long

ID	Runs	Label	Doc
etl	etl.cwl (Workflow)
get_hostname	../../tools/emit_hostname.cwl (CommandLineTool)
emit_bai_uuid	../../tools/emit_json_value.cwl (ExpressionTool)
emit_bam_uuid	../../tools/emit_json_value.cwl (ExpressionTool)
status_running	status_postgres.cwl (Workflow)
status_complete	status_postgres.cwl (Workflow)
emit_sqlite_uuid	../../tools/emit_json_value.cwl (ExpressionTool)
get_host_ipaddress	../../tools/emit_host_ipaddress.cwl (CommandLineTool)
get_host_macaddress	../../tools/emit_host_mac.cwl (CommandLineTool)
emit_mirna_profiling_tar_uuid	../../tools/emit_json_value.cwl (ExpressionTool)
emit_mirna_profiling_mirnas_quant_uuid	../../tools/emit_json_value.cwl (ExpressionTool)
emit_mirna_profiling_isoforms_quant_uuid	../../tools/emit_json_value.cwl (ExpressionTool)

ID	Type	Label	Doc
indexd_bai_uuid	String
indexd_bam_uuid	String
indexd_sqlite_uuid	String
indexd_mirna_profiling_tar_uuid	String
indexd_mirna_profiling_mirnas_quant_uuid	String
indexd_mirna_profiling_isoforms_quant_uuid	String