Path	Lines of Code
workflows/pipe-common/pipeline/__init__.py	5
workflows/pipe-common/pipeline/api/__init__.py	2
workflows/pipe-common/pipeline/api/api.py	1326
workflows/pipe-common/pipeline/api/datastorage.py	111
workflows/pipe-common/pipeline/api/json_parser.py	11
workflows/pipe-common/pipeline/api/region.py	55
workflows/pipe-common/pipeline/api/token.py	103
workflows/pipe-common/pipeline/autoscaling/__init__.py	14
workflows/pipe-common/pipeline/autoscaling/awsprovider.py	566
workflows/pipe-common/pipeline/autoscaling/azureprovider.py	505
workflows/pipe-common/pipeline/autoscaling/cloudprovider.py	26
workflows/pipe-common/pipeline/autoscaling/gcpprovider.py	341
workflows/pipe-common/pipeline/autoscaling/kubeprovider.py	178
workflows/pipe-common/pipeline/autoscaling/utils.py	348
workflows/pipe-common/pipeline/cluster/__init__.py	7
workflows/pipe-common/pipeline/cluster/cluster.py	110
workflows/pipe-common/pipeline/cluster/utils.py	31
workflows/pipe-common/pipeline/common/__init__.py	8
workflows/pipe-common/pipeline/common/common.py	71
workflows/pipe-common/pipeline/common/container.py	55
workflows/pipe-common/pipeline/common/kubernetes.py	28
workflows/pipe-common/pipeline/common/logged_command.py	144
workflows/pipe-common/pipeline/common/noverify_kubernetes.py	22
workflows/pipe-common/pipeline/common/pod.py	99
workflows/pipe-common/pipeline/common/samplesheet.py	61
workflows/pipe-common/pipeline/common/utils.py	15
workflows/pipe-common/pipeline/dts/__init__.py	2
workflows/pipe-common/pipeline/dts/dts.py	117
workflows/pipe-common/pipeline/dts/paths.py	22
workflows/pipe-common/pipeline/hpc/__init__.py	1
workflows/pipe-common/pipeline/hpc/autoscaler.py	436
workflows/pipe-common/pipeline/hpc/cloud.py	24
workflows/pipe-common/pipeline/hpc/cmd.py	20
workflows/pipe-common/pipeline/hpc/engine/__init__.py	1
workflows/pipe-common/pipeline/hpc/engine/gridengine.py	143
workflows/pipe-common/pipeline/hpc/engine/kube.py	242
workflows/pipe-common/pipeline/hpc/engine/sge.py	538
workflows/pipe-common/pipeline/hpc/engine/slurm.py	230
workflows/pipe-common/pipeline/hpc/event.py	40
workflows/pipe-common/pipeline/hpc/host.py	146
workflows/pipe-common/pipeline/hpc/instance/__init__.py	1
workflows/pipe-common/pipeline/hpc/instance/avail.py	38
workflows/pipe-common/pipeline/hpc/instance/provider.py	84
workflows/pipe-common/pipeline/hpc/instance/select.py	103
workflows/pipe-common/pipeline/hpc/logger.py	15
workflows/pipe-common/pipeline/hpc/param.py	282
workflows/pipe-common/pipeline/hpc/pipe.py	260
workflows/pipe-common/pipeline/hpc/resource.py	127
workflows/pipe-common/pipeline/hpc/utils.py	34
workflows/pipe-common/pipeline/hpc/valid.py	31
workflows/pipe-common/pipeline/log/__init__.py	1
workflows/pipe-common/pipeline/log/logger.py	291
workflows/pipe-common/pipeline/pipeline.py	407
workflows/pipe-common/pipeline/run_stats.py	62
workflows/pipe-common/pipeline/storage/__init__.py	1
workflows/pipe-common/pipeline/storage/storage.py	190
workflows/pipe-common/pipeline/utils/__init__.py	1
workflows/pipe-common/pipeline/utils/account.py	77
workflows/pipe-common/pipeline/utils/package.py	18
workflows/pipe-common/pipeline/utils/path.py	40
workflows/pipe-common/pipeline/utils/pki.py	23
workflows/pipe-common/pipeline/utils/plat.py	14
workflows/pipe-common/pipeline/utils/proc.py	9
workflows/pipe-common/pipeline/utils/profile.py	62
workflows/pipe-common/pipeline/utils/reg.py	18
workflows/pipe-common/pipeline/utils/ssh.py	75
workflows/pipe-common/powershell/ConfigureSystemSettings.ps1	23
workflows/pipe-common/powershell/FinalizeCloudDataConfig.ps1	20
workflows/pipe-common/powershell/MountDrive.ps1	85
workflows/pipe-common/powershell/RegisterCloudDataConfigurationTask.ps1	23
workflows/pipe-common/powershell/RegisterMountingTask.ps1	26
workflows/pipe-common/powershell/SetPlaceholderInFile.ps1	19
workflows/pipe-common/resources/linux/k8s-dind/cni_1.15.4_canal.yaml	732
workflows/pipe-common/resources/linux/k8s-dind/cni_1.28.2_flannel.yaml	218
workflows/pipe-common/scripts/__init__.py	1
workflows/pipe-common/scripts/add_root_certificate_win.py	15
workflows/pipe-common/scripts/autoscale_grid_engine.py	549
workflows/pipe-common/scripts/batch.py	183
workflows/pipe-common/scripts/blocked_users_cleanup.py	455
workflows/pipe-common/scripts/check_pipeline_permission.py	32
workflows/pipe-common/scripts/clone_pipeline.py	17
workflows/pipe-common/scripts/cluster_setup.py	191
workflows/pipe-common/scripts/cluster_wait_for_master.py	56
workflows/pipe-common/scripts/cluster_wait_for_node.py	105
workflows/pipe-common/scripts/cluster_wait_for_workers.py	123
workflows/pipe-common/scripts/commit_run.py	196
workflows/pipe-common/scripts/configure_cloud_data_win.py	34
workflows/pipe-common/scripts/configure_drive_mount_env_win.py	19
workflows/pipe-common/scripts/configure_nice_dcv_win.py	21
workflows/pipe-common/scripts/configure_nomachine_win.py	11
workflows/pipe-common/scripts/configure_seamless_logon_win.py	63
workflows/pipe-common/scripts/configure_shared_users.py	84
workflows/pipe-common/scripts/configure_system_settings_win.py	9
workflows/pipe-common/scripts/credentials_process.py	35
workflows/pipe-common/scripts/deps_graph.py	82
workflows/pipe-common/scripts/folder_batch.py	101
workflows/pipe-common/scripts/generate_sge_profiles.py	160
workflows/pipe-common/scripts/manage_sge_profiles.py	462
workflows/pipe-common/scripts/mount_storage.py	784
workflows/pipe-common/scripts/multi_sample_files_batch.py	76
workflows/pipe-common/scripts/profiles_credentials_writer.py	86
workflows/pipe-common/scripts/sample_sheet_batch.py	124
workflows/pipe-common/scripts/send_statistics.py	459
workflows/pipe-common/scripts/serve_desktop.py	180
workflows/pipe-common/scripts/sync_ngs_project.py	508
workflows/pipe-common/scripts/sync_users.py	385
workflows/pipe-common/scripts/token_expiration_refresher.py	83
workflows/pipe-common/scripts/transfer_parameters.py	615
workflows/pipe-common/scripts/watch_mount_shares.py	647
workflows/pipe-common/setup.py	53
workflows/pipe-demo/ngs/batch/src/run_analytical.py	84
workflows/pipe-demo/ngs/batch/src/run_demultiplex.py	53
workflows/pipe-demo/ngs/demultiplex/src/read_samples.py	14
workflows/pipe-demo/ngs/msgen/src/transfer_sources.py	56
workflows/pipe-demo/ngs/mutect2-gatk/src/mutect2gatk.wdl	714
workflows/pipe-demo/ngs/wes-analysis/src/collect_sample_metrics.py	232
workflows/pipe-demo/ngs/wes-analysis/src/collect_variant_metrics.py	87
workflows/pipe-templates/__AWS_HEALTHOMICS/AWS-HealthOmics-Workflow/src/workflow/main.nf	24
workflows/pipe-templates/__COMMON/cwl/src/@.cwl	11
workflows/pipe-templates/__COMMON/luigi/src/@.py	23
workflows/pipe-templates/__COMMON/nextflow/src/@.nf	11
workflows/pipe-templates/__COMMON/python/src/@.py	4
workflows/pipe-templates/__COMMON/wdl/src/@.wdl	8
workflows/pipe-templates/__SYSTEM/data_loader/src/model/__init__.py	1
workflows/pipe-templates/__SYSTEM/data_loader/src/model/base.py	45
workflows/pipe-templates/__SYSTEM/data_loader/src/model/entities_api.py	49
workflows/pipe-templates/__SYSTEM/data_loader/src/model/entity.py	17
workflows/pipe-templates/__SYSTEM/data_loader/src/sys-data-upload.py	154