cloudos-cli 2.17.0__py3-none-any.whl

cloudos_cli/__main__.py

@@ -0,0 +1,1297 @@
+#!/usr/bin/env python3
+
+import click
+import cloudos_cli.jobs.job as jb
+from cloudos_cli.clos import Cloudos
+from cloudos_cli.queue.queue import Queue
+import json
+import time
+import sys
+import os
+import urllib3
+from ._version import __version__
+from concurrent.futures import ThreadPoolExecutor, as_completed
+
+# GLOBAL VARS
+JOB_COMPLETED = 'completed'
+JOB_FAILED = 'failed'
+JOB_ABORTED = 'aborted'
+JOB_RUNNING = 'running'
+REQUEST_INTERVAL_CROMWELL = 30
+
+
+def ssl_selector(disable_ssl_verification, ssl_cert):
+    """Verify value selector.
+
+    This function stablish the value that will be passed to requests.verify
+    variable.
+
+    Parameters
+    ----------
+    disable_ssl_verification : bool
+        Whether to disable SSL verification.
+    ssl_cert : string
+        String indicating the path to the SSL certificate file to use.
+
+    Returns
+    -------
+    verify_ssl : [bool | string]
+        Either a bool or a path string to be passed to requests.verify to control
+        SSL verification.
+    """
+    if disable_ssl_verification:
+        verify_ssl = False
+        print('[WARNING] Disabling SSL verification')
+        urllib3.disable_warnings()
+    elif ssl_cert is None:
+        verify_ssl = True
+    elif os.path.isfile(ssl_cert):
+        verify_ssl = ssl_cert
+    else:
+        raise FileNotFoundError(f"The specified file '{ssl_cert}' was not found")
+    return verify_ssl
+
+
+@click.group()
+@click.version_option(__version__)
+def run_cloudos_cli():
+    """CloudOS python package: a package for interacting with CloudOS."""
+    print(run_cloudos_cli.__doc__ + '\n')
+    print('Version: ' + __version__ + '\n')
+
+
+@run_cloudos_cli.group()
+def job():
+    """CloudOS job functionality: run and check jobs in CloudOS."""
+    print(job.__doc__ + '\n')
+
+
+@run_cloudos_cli.group()
+def workflow():
+    """CloudOS workflow functionality: list and import workflows."""
+    print(workflow.__doc__ + '\n')
+
+
+@run_cloudos_cli.group()
+def project():
+    """CloudOS project functionality: list projects in CloudOS."""
+    print(project.__doc__ + '\n')
+
+
+@run_cloudos_cli.group()
+def cromwell():
+    """Cromwell server functionality: check status, start and stop."""
+    print(cromwell.__doc__ + '\n')
+
+
+@run_cloudos_cli.group()
+def queue():
+    """CloudOS job queue functionality."""
+    print(queue.__doc__ + '\n')
+
+
+@job.command('run')
+@click.option('-k',
+              '--apikey',
+              help='Your CloudOS API key',
+              required=True)
+@click.option('-c',
+              '--cloudos-url',
+              help=('The CloudOS url you are trying to access to. ' +
+                    'Default=https://cloudos.lifebit.ai.'),
+              default='https://cloudos.lifebit.ai')
+@click.option('--workspace-id',
+              help='The specific CloudOS workspace id.',
+              required=True)
+@click.option('--project-name',
+              help='The name of a CloudOS project.',
+              required=True)
+@click.option('--workflow-name',
+              help='The name of a CloudOS workflow or pipeline.',
+              required=True)
+@click.option('--job-config',
+              help=('A config file similar to a nextflow.config file, ' +
+                    'but only with the parameters to use with your job.'))
+@click.option('-p',
+              '--parameter',
+              multiple=True,
+              help=('A single parameter to pass to the job call. It should be in the ' +
+                    'following form: parameter_name=parameter_value. E.g.: ' +
+                    '-p input=s3://path_to_my_file. You can use this option as many ' +
+                    'times as parameters you want to include.'))
+@click.option('--nextflow-profile',
+              help=('A comma separated string indicating the nextflow profile/s ' +
+                    'to use with your job.'))
+@click.option('--nextflow-version',
+              help=('Nextflow version to use when executing the workflow in CloudOS. ' +
+                    'Please, note that versions above 22.10.8 are only DSL2 compatible. ' +
+                    'Default=22.10.8.'),
+              type=click.Choice(['22.10.8', '24.04.4', 'latest']),
+              default='22.10.8')
+@click.option('--git-commit',
+              help=('The exact whole 40 character commit hash to run for ' +
+                    'the selected pipeline. ' +
+                    'If not specified it defaults to the last commit ' +
+                    'of the default branch.'))
+@click.option('--git-tag',
+              help=('The tag to run for the selected pipeline. ' +
+                    'If not specified it defaults to the last commit ' +
+                    'of the default branch.'))
+@click.option('--job-name',
+              help='The name of the job. Default=new_job.',
+              default='new_job')
+@click.option('--resumable',
+              help='Whether to make the job able to be resumed or not.',
+              is_flag=True)
+@click.option('--do-not-save-logs',
+              help=('Avoids process log saving. If you select this option, your job process ' +
+                    'logs will not be stored.'),
+              is_flag=True)
+@click.option('--spot',
+              help=('[Deprecated in 2.11.0] This option has been deprecated and has no effect. ' +
+                    'Spot instances are no longer available in CloudOS.'),
+              is_flag=True)
+@click.option('--batch',
+              help=('[Deprecated in 2.7.0] Since v2.7.0, the default executor is AWSbatch ' +
+                    'so there is no need to use this flag. It is maintained for ' +
+                    'backwards compatibility.'),
+              is_flag=True)
+@click.option('--ignite',
+              help=('This flag allows running ignite executor if available. Please, note ' +
+                    'that ignite executor is being deprecated and may not be available in your ' +
+                    'CloudOS.'),
+              is_flag=True)
+@click.option('--job-queue',
+              help='Name of the job queue to use with a batch job.')
+@click.option('--instance-type',
+              help=('The type of execution platform compute instance to use. ' +
+                    'Default=c5.xlarge(aws)|Standard_D4as_v4(azure).'),
+              default='NONE_SELECTED')
+@click.option('--instance-disk',
+              help='The amount of disk storage to configure. Default=500.',
+              type=int,
+              default=500)
+@click.option('--storage-mode',
+              help=('Either \'lustre\' or \'regular\'. Indicates if the user wants to select ' +
+                    'regular or lustre storage. Default=regular.'),
+              default='regular')
+@click.option('--lustre-size',
+              help=('The lustre storage to be used when --storage-mode=lustre, in GB. It should ' +
+                    'be 1200 or a multiple of it. Default=1200.'),
+              type=int,
+              default=1200)
+@click.option('--wait-completion',
+              help=('Whether to wait to job completion and report final ' +
+                    'job status.'),
+              is_flag=True)
+@click.option('--wait-time',
+              help=('Max time to wait (in seconds) to job completion. ' +
+                    'Default=3600.'),
+              default=3600)
+@click.option('--wdl-mainfile',
+              help='For WDL workflows, which mainFile (.wdl) is configured to use.',)
+@click.option('--wdl-importsfile',
+              help='For WDL workflows, which importsFile (.zip) is configured to use.',)
+@click.option('-t',
+              '--cromwell-token',
+              help=('Specific Cromwell server authentication token. Currently, not necessary ' +
+                    'as apikey can be used instead, but maintained for backwards compatibility.'))
+@click.option('--repository-platform',
+              help='Name of the repository platform of the workflow. Default=github.',
+              default='github')
+@click.option('--execution-platform',
+              help='Name of the execution platform implemented in your CloudOS. Default=aws.',
+              type=click.Choice(['aws', 'azure', 'hpc']),
+              default='aws')
+@click.option('--hpc-id',
+              help=('ID of your HPC, only applicable when --execution-platform=hpc. ' +
+                    'Default=660fae20f93358ad61e0104b'),
+              default='660fae20f93358ad61e0104b')
+@click.option('--cost-limit',
+              help='Add a cost limit to your job. Default=30.0 (For no cost limit please use -1).',
+              type=float,
+              default=30.0)
+@click.option('--accelerate-file-staging',
+              help='Enables AWS S3 mountpoint for quicker file staging.',
+              is_flag=True)
+@click.option('--use-private-docker-repository',
+              help=('Allows to use private docker repository for running jobs. The Docker user ' +
+                    'account has to be already linked to CloudOS.'),
+              is_flag=True)
+@click.option('--verbose',
+              help='Whether to print information messages or not.',
+              is_flag=True)
+@click.option('--request-interval',
+              help=('Time interval to request (in seconds) the job status. ' +
+                    'For large jobs is important to use a high number to ' +
+                    'make fewer requests so that is not considered spamming by the API. ' +
+                    'Default=30.'),
+              default=30)
+@click.option('--disable-ssl-verification',
+              help=('Disable SSL certificate verification. Please, remember that this option is ' +
+                    'not generally recommended for security reasons.'),
+              is_flag=True)
+@click.option('--ssl-cert',
+              help='Path to your SSL certificate file.')
+def run(apikey,
+        cloudos_url,
+        workspace_id,
+        project_name,
+        workflow_name,
+        job_config,
+        parameter,
+        git_commit,
+        git_tag,
+        job_name,
+        resumable,
+        do_not_save_logs,
+        spot,
+        batch,
+        ignite,
+        job_queue,
+        nextflow_profile,
+        nextflow_version,
+        instance_type,
+        instance_disk,
+        storage_mode,
+        lustre_size,
+        wait_completion,
+        wait_time,
+        wdl_mainfile,
+        wdl_importsfile,
+        cromwell_token,
+        repository_platform,
+        execution_platform,
+        hpc_id,
+        cost_limit,
+        accelerate_file_staging,
+        use_private_docker_repository,
+        verbose,
+        request_interval,
+        disable_ssl_verification,
+        ssl_cert):
+    """Submit a job to CloudOS."""
+    cloudos_url = cloudos_url.rstrip('/')
+    verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
+    if spot:
+        print('[Message] You have specified spot instances but they are no longer available ' +
+              'in CloudOS. Option ignored.')
+    if do_not_save_logs:
+        save_logs = False
+    else:
+        save_logs = True
+    if instance_type == 'NONE_SELECTED':
+        if execution_platform == 'aws':
+            instance_type = 'c5.xlarge'
+        elif execution_platform == 'azure':
+            instance_type = 'Standard_D4as_v4'
+        else:
+            instance_type = None
+    if execution_platform == 'azure' or execution_platform == 'hpc':
+        batch = None
+    elif ignite:
+        batch = None
+        print('[Warning] You have specified ignite executor. Please, note that ignite is being ' +
+              'removed from CloudOS, so the command may fail. Check ignite availability in your ' +
+              'CloudOS')
+    else:
+        batch = True
+    if execution_platform == 'hpc':
+        print('\n[Message] HPC execution platform selected')
+        if hpc_id is None:
+            raise ValueError('Please, specify your HPC ID using --hpc parameter')
+        print('[Message] Please, take into account that HPC execution do not support ' +
+              'the following parameters and all of them will be ignored:\n' +
+              '\t--job-queue\n' +
+              '\t--resumable | --do-not-save-logs\n' +
+              '\t--instance-type | --instance-disk | --cost-limit\n' +
+              '\t--storage-mode | --lustre-size\n' +
+              '\t--wdl-mainfile | --wdl-importsfile | --cromwell-token\n')
+        wdl_mainfile = None
+        wdl_importsfile = None
+        storage_mode = 'regular'
+        save_logs = False
+    if accelerate_file_staging:
+        if execution_platform != 'aws':
+            print('[Message] You have selected accelerate file staging, but this function is ' +
+                  'only available when execution platform is AWS. The accelerate file staging ' +
+                  'will not be applied')
+            use_mountpoints = False
+        else:
+            use_mountpoints = True
+            print('[Message] Enabling AWS S3 mountpoint for accelerated file staging. ' +
+                  'Please, take into consideration the following:\n' +
+                  '\t- It significantly reduces runtime and compute costs but may increase network costs.\n' +
+                  '\t- Requires extra memory. Adjust process memory or optimise resource usage if necessary.\n' +
+                  '\t- This is still a CloudOS BETA feature.\n')
+    else:
+        use_mountpoints = False
+    if verbose:
+        print('\t...Detecting workflow type')
+    cl = Cloudos(cloudos_url, apikey, cromwell_token)
+    workflow_type = cl.detect_workflow(workflow_name, workspace_id, verify_ssl)
+    is_module = cl.is_module(workflow_name, workspace_id, verify_ssl)
+    if execution_platform == 'hpc' and workflow_type == 'wdl':
+        raise ValueError(f'The workflow {workflow_name} is a WDL workflow. ' +
+                         'WDL is not supported on HPC execution platform.')
+    if workflow_type == 'wdl':
+        print('[Message] WDL workflow detected')
+        if wdl_mainfile is None:
+            raise ValueError('Please, specify WDL mainFile using --wdl-mainfile <mainFile>.')
+        c_status = cl.get_cromwell_status(workspace_id, verify_ssl)
+        c_status_h = json.loads(c_status.content)["status"]
+        print(f'\tCurrent Cromwell server status is: {c_status_h}\n')
+        if c_status_h == 'Stopped':
+            print('\tStarting Cromwell server...\n')
+            cl.cromwell_switch(workspace_id, 'restart', verify_ssl)
+            elapsed = 0
+            while elapsed < 300 and c_status_h != 'Running':
+                c_status_old = c_status_h
+                time.sleep(REQUEST_INTERVAL_CROMWELL)
+                elapsed += REQUEST_INTERVAL_CROMWELL
+                c_status = cl.get_cromwell_status(workspace_id, verify_ssl)
+                c_status_h = json.loads(c_status.content)["status"]
+                if c_status_h != c_status_old:
+                    print(f'\tCurrent Cromwell server status is: {c_status_h}\n')
+        if c_status_h != 'Running':
+            raise Exception('Cromwell server did not restarted properly.')
+        cromwell_id = json.loads(c_status.content)["_id"]
+        print('\t' + ('*' * 80) + '\n' +
+              '\t[WARNING] Cromwell server is now running. Please, remember to stop it when ' +
+              'your\n' + '\tjob finishes. You can use the following command:\n' +
+              '\tcloudos cromwell stop \\\n' +
+              '\t\t--cromwell-token $CROMWELL_TOKEN \\\n' +
+              f'\t\t--cloudos-url {cloudos_url} \\\n' +
+              f'\t\t--workspace-id {workspace_id}\n' +
+              '\t' + ('*' * 80) + '\n')
+    else:
+        cromwell_id = None
+    if verbose:
+        print('\t...Preparing objects')
+    j = jb.Job(cloudos_url, apikey, None, workspace_id, project_name, workflow_name,
+               mainfile=wdl_mainfile, importsfile=wdl_importsfile,
+               repository_platform=repository_platform, verify=verify_ssl)
+    if verbose:
+        print('\tThe following Job object was created:')
+        print('\t' + str(j))
+        print('\t...Sending job to CloudOS\n')
+    if is_module:
+        if job_queue is not None:
+            print(f'[Message] Ignoring job queue "{job_queue}" for ' +
+                  f'Platform Workflow "{workflow_name}". Platform Workflows ' +
+                  'use their own predetermined queues.')
+        job_queue_id = None
+        if nextflow_version != '22.10.8':
+            print(f'[Message] The selected worflow \'{workflow_name}\' ' +
+                  'is a CloudOS module. CloudOS modules only work with ' +
+                  'Nextflow version 22.10.8. Switching to use 22.10.8')
+        nextflow_version = '22.10.8'
+    else:
+        queue = Queue(cloudos_url=cloudos_url, apikey=apikey, cromwell_token=cromwell_token,
+                      workspace_id=workspace_id, verify=verify_ssl)
+        job_queue_id = queue.fetch_job_queue_id(workflow_type=workflow_type, batch=batch,
+                                                job_queue=job_queue)
+    if use_private_docker_repository:
+        if is_module:
+            print(f'[Message] Workflow "{workflow_name}" is a CloudOS module. ' +
+                  'Option --use-private-docker-repository will be ignored.')
+            docker_login = False
+        else:
+            me = j.get_user_info(verify=verify_ssl)['dockerRegistriesCredentials']
+            if len(me) == 0:
+                raise Exception('User private Docker repository has been selected but your user ' +
+                                'credentials have not been configured yet. Please, link your ' +
+                                'Docker account to CloudOS before using ' +
+                                '--use-private-docker-repository option.')
+            print('[Message] Use private Docker repository has been selected. A custom job ' +
+                  'queue to support private Docker containers and/or Lustre FSx will be created for ' +
+                  'your job. The selected job queue will serve as a template.')
+            docker_login = True
+    else:
+        docker_login = False
+    if nextflow_version == 'latest':
+        nextflow_version = '24.04.4'
+        print('[Message] You have specified Nextflow version \'latest\'. The workflow will use the ' +
+              f'latest version available on CloudOS: {nextflow_version}.')
+    if nextflow_version != '22.10.8':
+        print(f'[Warning] You have specified Nextflow version {nextflow_version}. This version requires the pipeline ' +
+              'to be written in DSL2 and does not support DSL1.')
+    print('\nExecuting run...')
+    if workflow_type == 'nextflow':
+        print(f'\tNextflow version: {nextflow_version}')
+    j_id = j.send_job(job_config=job_config,
+                      parameter=parameter,
+                      git_commit=git_commit,
+                      git_tag=git_tag,
+                      job_name=job_name,
+                      resumable=resumable,
+                      save_logs=save_logs,
+                      batch=batch,
+                      job_queue_id=job_queue_id,
+                      nextflow_profile=nextflow_profile,
+                      nextflow_version=nextflow_version,
+                      instance_type=instance_type,
+                      instance_disk=instance_disk,
+                      storage_mode=storage_mode,
+                      lustre_size=lustre_size,
+                      execution_platform=execution_platform,
+                      hpc_id=hpc_id,
+                      workflow_type=workflow_type,
+                      cromwell_id=cromwell_id,
+                      cost_limit=cost_limit,
+                      use_mountpoints=use_mountpoints,
+                      docker_login=docker_login,
+                      verify=verify_ssl)
+    print(f'\tYour assigned job id is: {j_id}\n')
+    j_url = f'{cloudos_url}/app/jobs/{j_id}'
+    if wait_completion:
+        print('\tPlease, wait until job completion (max wait time of ' +
+              f'{wait_time} seconds).\n')
+        j_status = j.wait_job_completion(job_id=j_id,
+                                         wait_time=wait_time,
+                                         request_interval=request_interval,
+                                         verbose=verbose,
+                                         verify=verify_ssl)
+        j_name = j_status['name']
+        j_final_s = j_status['status']
+        if j_final_s == JOB_COMPLETED:
+            print(f'\nJob status for job "{j_name}" (ID: {j_id}): {j_final_s}')
+            sys.exit(0)
+        else:
+            print(f'\nJob status for job "{j_name}" (ID: {j_id}): {j_final_s}')
+            sys.exit(1)
+    else:
+        j_status = j.get_job_status(j_id, verify_ssl)
+        j_status_h = json.loads(j_status.content)["status"]
+        print(f'\tYour current job status is: {j_status_h}')
+        print('\tTo further check your job status you can either go to ' +
+              f'{j_url} or use the following command:\n' +
+              '\tcloudos job status \\\n' +
+              '\t\t--apikey $MY_API_KEY \\\n' +
+              f'\t\t--cloudos-url {cloudos_url} \\\n' +
+              f'\t\t--job-id {j_id}\n')
+
+
+@job.command('run-curated-examples')
+@click.option('-k',
+              '--apikey',
+              help='Your CloudOS API key',
+              required=True)
+@click.option('-c',
+              '--cloudos-url',
+              help=('The CloudOS url you are trying to access to. ' +
+                    'Default=https://cloudos.lifebit.ai.'),
+              default='https://cloudos.lifebit.ai')
+@click.option('--workspace-id',
+              help='The specific CloudOS workspace id.',
+              required=True)
+@click.option('--project-name',
+              help='The name of a CloudOS project.',
+              required=True)
+@click.option('--resumable',
+              help='Whether to make the job able to be resumed or not.',
+              is_flag=True)
+@click.option('--do-not-save-logs',
+              help=('Avoids process log saving. If you select this option, your job process ' +
+                    'logs will not be stored.'),
+              is_flag=True)
+@click.option('--spot',
+              help=('[Deprecated in 2.11.0] This option has been deprecated and has no effect. ' +
+                    'Spot instances are no longer available in CloudOS.'),
+              is_flag=True)
+@click.option('--batch',
+              help=('[Deprecated in 2.7.0] Since v2.7.0, the default executor is AWSbatch ' +
+                    'so there is no need to use this flag. It is maintained for ' +
+                    'backwards compatibility.'),
+              is_flag=True)
+@click.option('--ignite',
+              help=('This flag allows running ignite executor if available. Please, note ' +
+                    'that ignite executor is being deprecated and may not be available in your ' +
+                    'CloudOS.'),
+              is_flag=True)
+@click.option('--instance-type',
+              help=('The type of execution platform compute instance to use. ' +
+                    'Default=c5.xlarge(aws)|Standard_D4as_v4(azure).'),
+              default='NONE_SELECTED')
+@click.option('--instance-disk',
+              help='The amount of disk storage to configure. Default=500.',
+              type=int,
+              default=500)
+@click.option('--storage-mode',
+              help=('Either \'lustre\' or \'regular\'. Indicates if the user wants to select ' +
+                    'regular or lustre storage. Default=regular.'),
+              default='regular')
+@click.option('--lustre-size',
+              help=('The lustre storage to be used when --storage-mode=lustre, in GB. It should ' +
+                    'be 1200 or a multiple of it. Default=1200.'),
+              type=int,
+              default=1200)
+@click.option('--execution-platform',
+              help='Name of the execution platform implemented in your CloudOS. Default=aws.',
+              type=click.Choice(['aws', 'azure']),
+              default='aws')
+@click.option('--cost-limit',
+              help='Add a cost limit to your job. Default=30.0 (For no cost limit please use -1).',
+              type=float,
+              default=30.0)
+@click.option('--accelerate-file-staging',
+              help='Enables AWS S3 mountpoint for quicker file staging.',
+              is_flag=True)
+@click.option('--wait-completion',
+              help=('Whether to wait to job completion and report final ' +
+                    'job status.'),
+              is_flag=True)
+@click.option('--wait-time',
+              help=('Max time to wait (in seconds) to job completion. ' +
+                    'Default=3600.'),
+              default=3600)
+@click.option('--request-interval',
+              help=('Time interval to request (in seconds) the job status. ' +
+                    'For large jobs is important to use a high number to ' +
+                    'make fewer requests so that is not considered spamming by the API. ' +
+                    'Default=30.'),
+              default=30)
+@click.option('--verbose',
+              help='Whether to print information messages or not.',
+              is_flag=True)
+@click.option('--disable-ssl-verification',
+              help=('Disable SSL certificate verification. Please, remember that this option is ' +
+                    'not generally recommended for security reasons.'),
+              is_flag=True)
+@click.option('--ssl-cert',
+              help='Path to your SSL certificate file.')
+def run_curated_examples(apikey,
+                         cloudos_url,
+                         workspace_id,
+                         project_name,
+                         resumable,
+                         do_not_save_logs,
+                         spot,
+                         batch,
+                         ignite,
+                         instance_type,
+                         instance_disk,
+                         storage_mode,
+                         lustre_size,
+                         execution_platform,
+                         cost_limit,
+                         accelerate_file_staging,
+                         wait_completion,
+                         wait_time,
+                         request_interval,
+                         verbose,
+                         disable_ssl_verification,
+                         ssl_cert):
+    """Run all the curated workflows with example parameters.
+
+    NOTE that currently, only Nextflow workflows are supported.
+    """
+    cloudos_url = cloudos_url.rstrip('/')
+    verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
+    cl = Cloudos(cloudos_url, apikey, None)
+    curated_workflows = cl.get_curated_workflow_list(workspace_id, verify=verify_ssl)
+    job_id_list = []
+    runnable_curated_workflows = [
+        w for w in curated_workflows if w['workflowType'] == 'nextflow' and len(w['parameters']) > 0
+    ]
+    if spot:
+        print('\n[Message] You have specified spot instances but they are no longer available ' +
+              'in CloudOS. Option ignored.\n')
+    if do_not_save_logs:
+        save_logs = False
+    else:
+        save_logs = True
+    if instance_type == 'NONE_SELECTED':
+        if execution_platform == 'aws':
+            instance_type = 'c5.xlarge'
+        if execution_platform == 'azure':
+            instance_type = 'Standard_D4as_v4'
+    if execution_platform == 'azure':
+        batch = None
+    elif ignite:
+        batch = None
+        print('\n[Warning] You have specified ignite executor. Please, note that ignite is being ' +
+              'removed from CloudOS, so the command may fail. Check ignite availability in your ' +
+              'CloudOS\n')
+    else:
+        batch = True
+    if accelerate_file_staging:
+        if execution_platform != 'aws':
+            print('[Message] You have selected accelerate file staging, but this function is ' +
+                  'only available when execution platform is AWS. The accelerate file staging ' +
+                  'will not be applied')
+            use_mountpoints = False
+        else:
+            use_mountpoints = True
+            print('[Message] Enabling AWS S3 mountpoint for accelerated file staging. ' +
+                  'Please, take into consideration the following:\n' +
+                  '\t- It significantly reduces runtime and compute costs but may increase network costs.\n' +
+                  '\t- Requires extra memory. Adjust process memory or optimise resource usage if necessary.\n' +
+                  '\t- This is still a CloudOS BETA feature.\n')
+    else:
+        use_mountpoints = False
+    for workflow in runnable_curated_workflows:
+        workflow_name = workflow['name']
+        j = jb.Job(cloudos_url, apikey, None, workspace_id, project_name, workflow_name,
+                   repository_platform=workflow['repository']['platform'], verify=verify_ssl)
+        j_id = j.send_job(example_parameters=workflow['parameters'],
+                          job_name=f"{workflow['name']}|Example_Run",
+                          resumable=resumable,
+                          save_logs=save_logs,
+                          batch=batch,
+                          instance_type=instance_type,
+                          instance_disk=instance_disk,
+                          storage_mode=storage_mode,
+                          lustre_size=lustre_size,
+                          execution_platform=execution_platform,
+                          workflow_type='nextflow',
+                          cost_limit=cost_limit,
+                          use_mountpoints=use_mountpoints,
+                          verify=verify_ssl)
+        print(f'\tYour assigned job id is: {j_id}\n')
+        job_id_list.append(j_id)
+    print(f'\n\tAll {len(runnable_curated_workflows)} curated job launched successfully!\n')
+    if wait_completion:
+        print('\tPlease, wait until jobs completion (max wait time of ' +
+              f'{wait_time} seconds).\n')
+        # Multi-threaded api requests, max_workers is hard-coded to not allow for
+        # big numbers that can collapse API server.
+        threads = []
+        with ThreadPoolExecutor(max_workers=20) as executor:
+            for j in job_id_list:
+                threads.append(executor.submit(cl.wait_job_completion,
+                                               job_id=j,
+                                               wait_time=wait_time,
+                                               request_interval=request_interval,
+                                               verbose=verbose,
+                                               verify=verify_ssl)
+                               )
+        j_status_all = [task.result() for task in as_completed(threads)]
+        # Summary of job status
+        print("\n\tCurated example runs final status:\n")
+        for j_s in j_status_all:
+            j_name = j_s['name']
+            j_id = j_s['id']
+            j_status = j_s['status']
+            print(f'\t\tJob status for job "{j_name}" (ID: {j_id}): {j_status}')
+        successful_jobs = [j_s for j_s in j_status_all if j_s['status'] == JOB_COMPLETED]
+        failed_jobs = [j_s for j_s in j_status_all if j_s['status'] == JOB_FAILED]
+        aborted_jobs = [j_s for j_s in j_status_all if j_s['status'] == JOB_ABORTED]
+        running_jobs = [j_s for j_s in j_status_all if j_s['status'] == JOB_RUNNING]
+        print(f"""\n\tJob summary:
+              Successful jobs.....:  {len(successful_jobs)}
+              Failed jobs.........:  {len(failed_jobs)}
+              Jobs still running..:  {len(running_jobs)}
+              Aborted jobs........:  {len(aborted_jobs)}
+            -------------------------------
+              Total jobs..........:  {len(j_status_all)}""")
+
+
+@job.command('status')
+@click.option('-k',
+              '--apikey',
+              help='Your CloudOS API key',
+              required=True)
+@click.option('-c',
+              '--cloudos-url',
+              help=('The CloudOS url you are trying to access to. ' +
+                    'Default=https://cloudos.lifebit.ai.'),
+              default='https://cloudos.lifebit.ai')
+@click.option('--job-id',
+              help='The job id in CloudOS to search for.',
+              required=True)
+@click.option('--verbose',
+              help='Whether to print information messages or not.',
+              is_flag=True)
+@click.option('--disable-ssl-verification',
+              help=('Disable SSL certificate verification. Please, remember that this option is ' +
+                    'not generally recommended for security reasons.'),
+              is_flag=True)
+@click.option('--ssl-cert',
+              help='Path to your SSL certificate file.')
+def job_status(apikey,
+               cloudos_url,
+               job_id,
+               verbose,
+               disable_ssl_verification,
+               ssl_cert):
+    """Check job status in CloudOS."""
+    cloudos_url = cloudos_url.rstrip('/')
+    print('Executing status...')
+    verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
+    if verbose:
+        print('\t...Preparing objects')
+    cl = Cloudos(cloudos_url, apikey, None)
+    if verbose:
+        print('\tThe following Cloudos object was created:')
+        print('\t' + str(cl) + '\n')
+        print(f'\tSearching for job id: {job_id}')
+    j_status = cl.get_job_status(job_id, verify_ssl)
+    j_status_h = json.loads(j_status.content)["status"]
+    print(f'\tYour current job status is: {j_status_h}\n')
+    j_url = f'{cloudos_url}/app/jobs/{job_id}'
+    print(f'\tTo further check your job status you can either go to {j_url} ' +
+          'or repeat the command you just used.')
+
+
+@job.command('list')
+@click.option('-k',
+              '--apikey',
+              help='Your CloudOS API key',
+              required=True)
+@click.option('-c',
+              '--cloudos-url',
+              help=('The CloudOS url you are trying to access to. ' +
+                    'Default=https://cloudos.lifebit.ai.'),
+              default='https://cloudos.lifebit.ai')
+@click.option('--workspace-id',
+              help='The specific CloudOS workspace id.',
+              required=True)
+@click.option('--output-basename',
+              help=('Output file base name to save jobs list. ' +
+                    'Default=joblist'),
+              default='joblist',
+              required=False)
+@click.option('--output-format',
+              help='The desired file format (file extension) for the output. Default=csv.',
+              type=click.Choice(['csv', 'json'], case_sensitive=False),
+              default='csv')
+@click.option('--all-fields',
+              help=('Whether to collect all available fields from jobs or ' +
+                    'just the preconfigured selected fields. Only applicable ' +
+                    'when --output-format=csv'),
+              is_flag=True)
+@click.option('--last-n-jobs',
+              help=("The number of last user's jobs to retrieve. You can use 'all' to " +
+                    "retrieve all user's jobs. Default=30."),
+              default='30')
+@click.option('--page',
+              help=('Response page to retrieve. If --last-n-jobs is set, then --page ' +
+                    'value corresponds to the first page to retrieve. Default=1.'),
+              type=int,
+              default=1)
+@click.option('--archived',
+              help=('When this flag is used, only archived jobs list is collected.'),
+              is_flag=True)
+@click.option('--verbose',
+              help='Whether to print information messages or not.',
+              is_flag=True)
+@click.option('--disable-ssl-verification',
+              help=('Disable SSL certificate verification. Please, remember that this option is ' +
+                    'not generally recommended for security reasons.'),
+              is_flag=True)
+@click.option('--ssl-cert',
+              help='Path to your SSL certificate file.')
+def list_jobs(apikey,
+              cloudos_url,
+              workspace_id,
+              output_basename,
+              output_format,
+              all_fields,
+              last_n_jobs,
+              page,
+              archived,
+              verbose,
+              disable_ssl_verification,
+              ssl_cert):
+    """Collect all your jobs from a CloudOS workspace in CSV format."""
+    cloudos_url = cloudos_url.rstrip('/')
+    verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
+    outfile = output_basename + '.' + output_format
+    print('Executing list...')
+    if verbose:
+        print('\t...Preparing objects')
+    cl = Cloudos(cloudos_url, apikey, None)
+    if verbose:
+        print('\tThe following Cloudos object was created:')
+        print('\t' + str(cl) + '\n')
+        print('\tSearching for jobs in the following workspace: ' +
+              f'{workspace_id}')
+    if last_n_jobs != 'all':
+        try:
+            last_n_jobs = int(last_n_jobs)
+        except ValueError:
+            print("[ERROR] last-n-jobs value was not valid. Please use a positive int or 'all'")
+            raise
+    my_jobs_r = cl.get_job_list(workspace_id, last_n_jobs, page, archived, verify_ssl)
+    if output_format == 'csv':
+        my_jobs = cl.process_job_list(my_jobs_r, all_fields)
+        my_jobs.to_csv(outfile, index=False)
+        print(f'\tJob list collected with a total of {my_jobs.shape[0]} jobs.')
+    elif output_format == 'json':
+        with open(outfile, 'w') as o:
+            o.write(json.dumps(my_jobs_r))
+        print(f'\tJob list collected with a total of {len(my_jobs_r)} jobs.')
+    else:
+        raise ValueError('Unrecognised output format. Please use one of [csv|json]')
+    print(f'\tJob list saved to {outfile}')
+
+
+@workflow.command('list')
+@click.option('-k',
+              '--apikey',
+              help='Your CloudOS API key',
+              required=True)
+@click.option('-c',
+              '--cloudos-url',
+              help=('The CloudOS url you are trying to access to. ' +
+                    'Default=https://cloudos.lifebit.ai.'),
+              default='https://cloudos.lifebit.ai')
+@click.option('--workspace-id',
+              help='The specific CloudOS workspace id.',
+              required=True)
+@click.option('--output-basename',
+              help=('Output file base name to save workflow list. ' +
+                    'Default=workflow_list'),
+              default='workflow_list',
+              required=False)
+@click.option('--output-format',
+              help='The desired file format (file extension) for the output. Default=csv.',
+              type=click.Choice(['csv', 'json'], case_sensitive=False),
+              default='csv')
+@click.option('--all-fields',
+              help=('Whether to collect all available fields from workflows or ' +
+                    'just the preconfigured selected fields. Only applicable ' +
+                    'when --output-format=csv'),
+              is_flag=True)
+@click.option('--curated',
+              help='Whether to collect curated workflows only.',
+              is_flag=True)
+@click.option('--verbose',
+              help='Whether to print information messages or not.',
+              is_flag=True)
+@click.option('--disable-ssl-verification',
+              help=('Disable SSL certificate verification. Please, remember that this option is ' +
+                    'not generally recommended for security reasons.'),
+              is_flag=True)
+@click.option('--ssl-cert',
+              help='Path to your SSL certificate file.')
+def list_workflows(apikey,
+                   cloudos_url,
+                   workspace_id,
+                   output_basename,
+                   output_format,
+                   all_fields,
+                   curated,
+                   verbose,
+                   disable_ssl_verification,
+                   ssl_cert):
+    """Collect all workflows from a CloudOS workspace in CSV format."""
+    cloudos_url = cloudos_url.rstrip('/')
+    verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
+    outfile = output_basename + '.' + output_format
+    print('Executing list...')
+    if verbose:
+        print('\t...Preparing objects')
+    cl = Cloudos(cloudos_url, apikey, None)
+    if verbose:
+        print('\tThe following Cloudos object was created:')
+        print('\t' + str(cl) + '\n')
+        print('\tSearching for workflows in the following workspace: ' +
+              f'{workspace_id}')
+    if curated:
+        my_workflows_r = cl.get_curated_workflow_list(workspace_id, verify=verify_ssl)
+    else:
+        my_workflows_r = cl.get_workflow_list(workspace_id, verify=verify_ssl)
+    if output_format == 'csv':
+        my_workflows = cl.process_workflow_list(my_workflows_r, all_fields)
+        my_workflows.to_csv(outfile, index=False)
+        print(f'\tWorkflow list collected with a total of {my_workflows.shape[0]} workflows.')
+    elif output_format == 'json':
+        with open(outfile, 'w') as o:
+            o.write(json.dumps(my_workflows_r))
+        print(f'\tWorkflow list collected with a total of {len(my_workflows_r)} workflows.')
+    else:
+        raise ValueError('Unrecognised output format. Please use one of [csv|json]')
+    print(f'\tWorkflow list saved to {outfile}')
+
+
+@workflow.command('import')
+@click.option('-k',
+              '--apikey',
+              help='Your CloudOS API key',
+              required=True)
+@click.option('-c',
+              '--cloudos-url',
+              help=('The CloudOS url you are trying to access to. ' +
+                    'Default=https://cloudos.lifebit.ai.'),
+              default='https://cloudos.lifebit.ai')
+@click.option('--workspace-id',
+              help='The specific CloudOS workspace id.',
+              required=True)
+@click.option('--workflow-url',
+              help=('URL of the workflow to import. Please, note that it should ' +
+                    'be the URL shown in the browser, and it should come without ' +
+                    'any of the .git or /browse extensions.'),
+              required=True)
+@click.option('--workflow-name',
+              help="The name that the workflow will have in CloudOS",
+              required=True)
+@click.option('--workflow-docs-link',
+              help="Workflow documentation URL.",
+              default='')
+@click.option('--repository-project-id',
+              type=int,
+              help="The ID of your repository project",
+              required=True)
+@click.option('--repository-id',
+              type=int,
+              help="The ID of your repository. Only required for GitHub repositories")
+@click.option('--disable-ssl-verification',
+              help=('Disable SSL certificate verification. Please, remember that this option is ' +
+                    'not generally recommended for security reasons.'),
+              is_flag=True)
+@click.option('--ssl-cert',
+              help='Path to your SSL certificate file.')
+def import_workflows(apikey,
+                     cloudos_url,
+                     workspace_id,
+                     workflow_url,
+                     workflow_name,
+                     repository_project_id,
+                     workflow_docs_link,
+                     repository_id,
+                     disable_ssl_verification,
+                     ssl_cert):
+    """Imports workflows to CloudOS."""
+    cloudos_url = cloudos_url.rstrip('/')
+    verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
+    print('Executing workflow import...\n')
+    print('\t[Message] Only Nextflow workflows are currently supported.\n')
+    cl = Cloudos(cloudos_url, apikey, None)
+    workflow_id = cl.workflow_import(workspace_id,
+                                     workflow_url,
+                                     workflow_name,
+                                     repository_project_id,
+                                     workflow_docs_link,
+                                     repository_id,
+                                     verify=verify_ssl)
+    print(f'\tWorkflow {workflow_name} was imported successfully with the ' +
+          f'following ID: {workflow_id}')
+
+
+@project.command('list')
+@click.option('-k',
+              '--apikey',
+              help='Your CloudOS API key',
+              required=True)
+@click.option('-c',
+              '--cloudos-url',
+              help=('The CloudOS url you are trying to access to. ' +
+                    'Default=https://cloudos.lifebit.ai.'),
+              default='https://cloudos.lifebit.ai')
+@click.option('--workspace-id',
+              help='The specific CloudOS workspace id.',
+              required=True)
+@click.option('--output-basename',
+              help=('Output file base name to save project list. ' +
+                    'Default=project_list'),
+              default='project_list',
+              required=False)
+@click.option('--output-format',
+              help='The desired file format (file extension) for the output. Default=csv.',
+              type=click.Choice(['csv', 'json'], case_sensitive=False),
+              default='csv')
+@click.option('--all-fields',
+              help=('Whether to collect all available fields from projects or ' +
+                    'just the preconfigured selected fields. Only applicable ' +
+                    'when --output-format=csv'),
+              is_flag=True)
+@click.option('--verbose',
+              help='Whether to print information messages or not.',
+              is_flag=True)
+@click.option('--disable-ssl-verification',
+              help=('Disable SSL certificate verification. Please, remember that this option is ' +
+                    'not generally recommended for security reasons.'),
+              is_flag=True)
+@click.option('--ssl-cert',
+              help='Path to your SSL certificate file.')
+def list_projects(apikey,
+                  cloudos_url,
+                  workspace_id,
+                  output_basename,
+                  output_format,
+                  all_fields,
+                  verbose,
+                  disable_ssl_verification,
+                  ssl_cert):
+    """Collect all projects from a CloudOS workspace in CSV format."""
+    cloudos_url = cloudos_url.rstrip('/')
+    verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
+    outfile = output_basename + '.' + output_format
+    print('Executing list...')
+    if verbose:
+        print('\t...Preparing objects')
+    cl = Cloudos(cloudos_url, apikey, None)
+    if verbose:
+        print('\tThe following Cloudos object was created:')
+        print('\t' + str(cl) + '\n')
+        print('\tSearching for projects in the following workspace: ' +
+              f'{workspace_id}')
+    my_projects_r = cl.get_project_list(workspace_id, verify_ssl)
+    if output_format == 'csv':
+        my_projects = cl.process_project_list(my_projects_r, all_fields)
+        my_projects.to_csv(outfile, index=False)
+        print(f'\tProject list collected with a total of {my_projects.shape[0]} projects.')
+    elif output_format == 'json':
+        with open(outfile, 'w') as o:
+            o.write(my_projects_r.text)
+        content = json.loads(my_projects_r.content)
+        if 'projects' in content:
+            content_l = len(content['projects'])
+        else:
+            content_l = len(content)
+        print('\tProject list collected with a total of ' +
+              f'{content_l} projects.')
+    else:
+        raise ValueError('Unrecognised output format. Please use one of [csv|json]')
+    print(f'\tProject list saved to {outfile}')
+
+
+@cromwell.command('status')
+@click.version_option()
+@click.option('-k',
+              '--apikey',
+              help='Your CloudOS API key.')
+@click.option('-t',
+              '--cromwell-token',
+              help=('Specific Cromwell server authentication token. You can use it instead of ' +
+                    'the apikey.'))
+@click.option('-c',
+              '--cloudos-url',
+              help=('The CloudOS url you are trying to access to. ' +
+                    'Default=https://cloudos.lifebit.ai.'),
+              default='https://cloudos.lifebit.ai')
+@click.option('--workspace-id',
+              help='The specific CloudOS workspace id.',
+              required=True)
+@click.option('--verbose',
+              help='Whether to print information messages or not.',
+              is_flag=True)
+@click.option('--disable-ssl-verification',
+              help=('Disable SSL certificate verification. Please, remember that this option is ' +
+                    'not generally recommended for security reasons.'),
+              is_flag=True)
+@click.option('--ssl-cert',
+              help='Path to your SSL certificate file.')
+def cromwell_status(apikey,
+                    cromwell_token,
+                    cloudos_url,
+                    workspace_id,
+                    verbose,
+                    disable_ssl_verification,
+                    ssl_cert):
+    """Check Cromwell server status in CloudOS."""
+    cloudos_url = cloudos_url.rstrip('/')
+    if apikey is None and cromwell_token is None:
+        raise ValueError("Please, use one of the following tokens: '--apikey', '--cromwell_token'")
+    print('Executing status...')
+    verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
+    if verbose:
+        print('\t...Preparing objects')
+    cl = Cloudos(cloudos_url, apikey, cromwell_token)
+    if verbose:
+        print('\tThe following Cloudos object was created:')
+        print('\t' + str(cl) + '\n')
+        print(f'\tChecking Cromwell status in {workspace_id} workspace')
+    c_status = cl.get_cromwell_status(workspace_id, verify_ssl)
+    c_status_h = json.loads(c_status.content)["status"]
+    print(f'\tCurrent Cromwell server status is: {c_status_h}\n')
+
+
+@cromwell.command('start')
+@click.version_option()
+@click.option('-k',
+              '--apikey',
+              help='Your CloudOS API key.')
+@click.option('-t',
+              '--cromwell-token',
+              help=('Specific Cromwell server authentication token. You can use it instead of ' +
+                    'the apikey.'))
+@click.option('-c',
+              '--cloudos-url',
+              help=('The CloudOS url you are trying to access to. ' +
+                    'Default=https://cloudos.lifebit.ai.'),
+              default='https://cloudos.lifebit.ai')
+@click.option('--workspace-id',
+              help='The specific CloudOS workspace id.',
+              required=True)
+@click.option('--wait-time',
+              help=('Max time to wait (in seconds) to Cromwell restart. ' +
+                    'Default=300.'),
+              default=300)
+@click.option('--verbose',
+              help='Whether to print information messages or not.',
+              is_flag=True)
+@click.option('--disable-ssl-verification',
+              help=('Disable SSL certificate verification. Please, remember that this option is ' +
+                    'not generally recommended for security reasons.'),
+              is_flag=True)
+@click.option('--ssl-cert',
+              help='Path to your SSL certificate file.')
+def cromwell_restart(apikey,
+                     cromwell_token,
+                     cloudos_url,
+                     workspace_id,
+                     wait_time,
+                     verbose,
+                     disable_ssl_verification,
+                     ssl_cert):
+    """Restart Cromwell server in CloudOS."""
+    cloudos_url = cloudos_url.rstrip('/')
+    if apikey is None and cromwell_token is None:
+        raise ValueError("Please, use one of the following tokens: '--apikey', '--cromwell_token'")
+    verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
+    action = 'restart'
+    print('Starting Cromwell server...')
+    if verbose:
+        print('\t...Preparing objects')
+    cl = Cloudos(cloudos_url, apikey, cromwell_token)
+    if verbose:
+        print('\tThe following Cloudos object was created:')
+        print('\t' + str(cl) + '\n')
+        print(f'\tStarting Cromwell server in {workspace_id} workspace')
+    cl.cromwell_switch(workspace_id, action, verify_ssl)
+    c_status = cl.get_cromwell_status(workspace_id, verify_ssl)
+    c_status_h = json.loads(c_status.content)["status"]
+    print(f'\tCurrent Cromwell server status is: {c_status_h}\n')
+    elapsed = 0
+    while elapsed < wait_time and c_status_h != 'Running':
+        c_status_old = c_status_h
+        time.sleep(REQUEST_INTERVAL_CROMWELL)
+        elapsed += REQUEST_INTERVAL_CROMWELL
+        c_status = cl.get_cromwell_status(workspace_id, verify_ssl)
+        c_status_h = json.loads(c_status.content)["status"]
+        if c_status_h != c_status_old:
+            print(f'\tCurrent Cromwell server status is: {c_status_h}\n')
+    if c_status_h != 'Running':
+        print(f'\tYour current Cromwell status is: {c_status_h}. The ' +
+              f'selected wait-time of {wait_time} was exceeded. Please, ' +
+              'consider to set a longer wait-time.')
+        print('\tTo further check your Cromwell status you can either go to ' +
+              f'{cloudos_url} or use the following command:\n' +
+              '\tcloudos cromwell status \\\n' +
+              f'\t\t--cloudos-url {cloudos_url} \\\n' +
+              '\t\t--cromwell-token $CROMWELL_TOKEN \\\n' +
+              f'\t\t--workspace-id {workspace_id}')
+        sys.exit(1)
+
+
+@cromwell.command('stop')
+@click.version_option()
+@click.option('-k',
+              '--apikey',
+              help='Your CloudOS API key.')
+@click.option('-t',
+              '--cromwell-token',
+              help=('Specific Cromwell server authentication token. You can use it instead of ' +
+                    'the apikey.'))
+@click.option('-c',
+              '--cloudos-url',
+              help=('The CloudOS url you are trying to access to. ' +
+                    'Default=https://cloudos.lifebit.ai.'),
+              default='https://cloudos.lifebit.ai')
+@click.option('--workspace-id',
+              help='The specific CloudOS workspace id.',
+              required=True)
+@click.option('--verbose',
+              help='Whether to print information messages or not.',
+              is_flag=True)
+@click.option('--disable-ssl-verification',
+              help=('Disable SSL certificate verification. Please, remember that this option is ' +
+                    'not generally recommended for security reasons.'),
+              is_flag=True)
+@click.option('--ssl-cert',
+              help='Path to your SSL certificate file.')
+def cromwell_stop(apikey,
+                  cromwell_token,
+                  cloudos_url,
+                  workspace_id,
+                  verbose,
+                  disable_ssl_verification,
+                  ssl_cert):
+    """Stop Cromwell server in CloudOS."""
+    cloudos_url = cloudos_url.rstrip('/')
+    if apikey is None and cromwell_token is None:
+        raise ValueError("Please, use one of the following tokens: '--apikey', '--cromwell_token'")
+    verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
+    action = 'stop'
+    print('Stopping Cromwell server...')
+    if verbose:
+        print('\t...Preparing objects')
+    cl = Cloudos(cloudos_url, apikey, cromwell_token)
+    if verbose:
+        print('\tThe following Cloudos object was created:')
+        print('\t' + str(cl) + '\n')
+        print(f'\tStopping Cromwell server in {workspace_id} workspace')
+    cl.cromwell_switch(workspace_id, action, verify_ssl)
+    c_status = cl.get_cromwell_status(workspace_id, verify_ssl)
+    c_status_h = json.loads(c_status.content)["status"]
+    print(f'\tCurrent Cromwell server status is: {c_status_h}\n')
+
+
+@queue.command('list')
+@click.option('-k',
+              '--apikey',
+              help='Your CloudOS API key',
+              required=True)
+@click.option('-c',
+              '--cloudos-url',
+              help=('The CloudOS url you are trying to access to. ' +
+                    'Default=https://cloudos.lifebit.ai.'),
+              default='https://cloudos.lifebit.ai')
+@click.option('--workspace-id',
+              help='The specific CloudOS workspace id.',
+              required=True)
+@click.option('--output-basename',
+              help=('Output file base name to save job queue list. ' +
+                    'Default=job_queue_list'),
+              default='job_queue_list',
+              required=False)
+@click.option('--output-format',
+              help='The desired file format (file extension) for the output. Default=csv.',
+              type=click.Choice(['csv', 'json'], case_sensitive=False),
+              default='csv')
+@click.option('--all-fields',
+              help=('Whether to collect all available fields from workflows or ' +
+                    'just the preconfigured selected fields. Only applicable ' +
+                    'when --output-format=csv'),
+              is_flag=True)
+@click.option('--disable-ssl-verification',
+              help=('Disable SSL certificate verification. Please, remember that this option is ' +
+                    'not generally recommended for security reasons.'),
+              is_flag=True)
+@click.option('--ssl-cert',
+              help='Path to your SSL certificate file.')
+def list_queues(apikey,
+                cloudos_url,
+                workspace_id,
+                output_basename,
+                output_format,
+                all_fields,
+                disable_ssl_verification,
+                ssl_cert):
+    """Collect all available job queues from a CloudOS workspace."""
+    cloudos_url = cloudos_url.rstrip('/')
+    verify_ssl = ssl_selector(disable_ssl_verification, ssl_cert)
+    outfile = output_basename + '.' + output_format
+    print('Executing list...')
+    j_queue = Queue(cloudos_url, apikey, None, workspace_id, verify=verify_ssl)
+    my_queues = j_queue.get_job_queues()
+    if len(my_queues) == 0:
+        raise ValueError('No AWS batch queues found. Please, make sure that your CloudOS supports AWS bath queues')
+    if output_format == 'csv':
+        queues_processed = j_queue.process_queue_list(my_queues, all_fields)
+        queues_processed.to_csv(outfile, index=False)
+        print(f'\tJob queue list collected with a total of {queues_processed.shape[0]} queues.')
+    elif output_format == 'json':
+        with open(outfile, 'w') as o:
+            o.write(json.dumps(my_queues))
+        print(f'\tJob queue list collected with a total of {len(my_queues)} queues.')
+    else:
+        raise ValueError('Unrecognised output format. Please use one of [csv|json]')
+    print(f'\tJob queue list saved to {outfile}')
+
+
+if __name__ == "__main__":
+    run_cloudos_cli()