cloudos-cli 2.87.1__tar.gz → 2.88.1__tar.gz

{cloudos_cli-2.87.1 → cloudos_cli-2.88.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.87.1
+Version: 2.88.1
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -687,6 +687,29 @@ When there are duplicate `--workflow-name` in the platform, you can add the `--l
 
 _For example, the pipeline `lifebit-process` was imported on May 23 2025 and again on May 30 2025; with the `--last` flag, it will use the import of May 30, 2025._
 
+**Nextflow Version Support**
+
+CloudOS CLI supports multiple Nextflow versions, with intelligent defaults based on your workflow type and execution platform.
+
+**Default Version Behavior:**
+
+The default Nextflow version is automatically selected based on your workflow type and execution platform:
+
+- **Azure Platform**: Always uses `22.11.1-edge` regardless of workflow type
+- **Platform Workflows** (AWS/HPC): Uses `22.10.8` (Lifebit provided workflows and modules)
+- **User-Imported Workflows** (AWS/HPC): AWS uses `24.04.4`; HPC uses `22.10.8`
+
+**Specifying a Custom Version:**
+
+You can override the default by using the `--nextflow-version` parameter:
+
+```bash
+cloudos job run --profile my_profile --workflow-name rnatoy --job-config cloudos_cli/examples/rnatoy.config --nextflow-version 25.04.8 --resumable
+```
+
+> [!NOTE]
+> **Azure Platform Behavior**: If you specify a Nextflow version not supported by Azure (anything other than 22.11.1-edge), CloudOS CLI will display a warning and automatically use 22.11.1-edge instead. Your job will proceed without error.
+
 **AWS Executor Support**
 
 CloudOS supports [AWS batch](https://www.nextflow.io/docs/latest/executor.html?highlight=executors#aws-batch) executor by default.
@@ -705,6 +728,7 @@ cloudos job run --profile my_profile --workflow-name rnatoy --job-config cloudos
 CloudOS can also be configured to use Microsoft Azure compute platforms. If your CloudOS is configured to use Azure, you will need to take into consideration the following:
 
 - When sending jobs to CloudOS using `cloudos job run` command, please use the option `--execution-platform azure`
+- Azure only supports Nextflow version `22.11.1-edge`. If you specify a different version, CloudOS CLI will display a warning and automatically use `22.11.1-edge` instead
 - Due to the lack of AWS batch queues in Azure, `cloudos queue list` command is not working
 
 Other than that, `cloudos-cli` will work very similarly. For instance, this is a typical send job command:
@@ -2154,7 +2178,7 @@ cloudos interactive-session create \
 - `--spot`: Use spot instances (AWS only, cost-saving)
 - `--shared`: Make session accessible to workspace members
 - `--cost-limit`: Compute cost limit in USD (default: -1 for unlimited)
-- `--shutdown-in`: Auto-shutdown duration (e.g., `8h`, `2d`, `30m`)
+- `--shutdown-in`: Auto-shutdown duration (e.g., `8h`, `2d`, `30m`, default: `12h`)
 
 **Data & Storage Management:**
 - `--mount`: Mount a data file into the session. Supports both CloudOS datasets and S3 files (AWS only). Format: `project_name/dataset_path` (e.g., `leila-test/Data/file.csv`) or `s3://bucket/path/to/file` (e.g., `s3://my-bucket/data/file.csv`). Can be used multiple times.

{cloudos_cli-2.87.1 → cloudos_cli-2.88.1}/README.md

@@ -652,6 +652,29 @@ When there are duplicate `--workflow-name` in the platform, you can add the `--l
 
 _For example, the pipeline `lifebit-process` was imported on May 23 2025 and again on May 30 2025; with the `--last` flag, it will use the import of May 30, 2025._
 
+**Nextflow Version Support**
+
+CloudOS CLI supports multiple Nextflow versions, with intelligent defaults based on your workflow type and execution platform.
+
+**Default Version Behavior:**
+
+The default Nextflow version is automatically selected based on your workflow type and execution platform:
+
+- **Azure Platform**: Always uses `22.11.1-edge` regardless of workflow type
+- **Platform Workflows** (AWS/HPC): Uses `22.10.8` (Lifebit provided workflows and modules)
+- **User-Imported Workflows** (AWS/HPC): AWS uses `24.04.4`; HPC uses `22.10.8`
+
+**Specifying a Custom Version:**
+
+You can override the default by using the `--nextflow-version` parameter:
+
+```bash
+cloudos job run --profile my_profile --workflow-name rnatoy --job-config cloudos_cli/examples/rnatoy.config --nextflow-version 25.04.8 --resumable
+```
+
+> [!NOTE]
+> **Azure Platform Behavior**: If you specify a Nextflow version not supported by Azure (anything other than 22.11.1-edge), CloudOS CLI will display a warning and automatically use 22.11.1-edge instead. Your job will proceed without error.
+
 **AWS Executor Support**
 
 CloudOS supports [AWS batch](https://www.nextflow.io/docs/latest/executor.html?highlight=executors#aws-batch) executor by default.
@@ -670,6 +693,7 @@ cloudos job run --profile my_profile --workflow-name rnatoy --job-config cloudos
 CloudOS can also be configured to use Microsoft Azure compute platforms. If your CloudOS is configured to use Azure, you will need to take into consideration the following:
 
 - When sending jobs to CloudOS using `cloudos job run` command, please use the option `--execution-platform azure`
+- Azure only supports Nextflow version `22.11.1-edge`. If you specify a different version, CloudOS CLI will display a warning and automatically use `22.11.1-edge` instead
 - Due to the lack of AWS batch queues in Azure, `cloudos queue list` command is not working
 
 Other than that, `cloudos-cli` will work very similarly. For instance, this is a typical send job command:
@@ -2119,7 +2143,7 @@ cloudos interactive-session create \
 - `--spot`: Use spot instances (AWS only, cost-saving)
 - `--shared`: Make session accessible to workspace members
 - `--cost-limit`: Compute cost limit in USD (default: -1 for unlimited)
-- `--shutdown-in`: Auto-shutdown duration (e.g., `8h`, `2d`, `30m`)
+- `--shutdown-in`: Auto-shutdown duration (e.g., `8h`, `2d`, `30m`, default: `12h`)
 
 **Data & Storage Management:**
 - `--mount`: Mount a data file into the session. Supports both CloudOS datasets and S3 files (AWS only). Format: `project_name/dataset_path` (e.g., `leila-test/Data/file.csv`) or `s3://bucket/path/to/file` (e.g., `s3://my-bucket/data/file.csv`). Can be used multiple times.

cloudos_cli-2.88.1/cloudos_cli/_version.py

@@ -0,0 +1 @@
+__version__ = '2.88.1'

{cloudos_cli-2.87.1 → cloudos_cli-2.88.1}/cloudos_cli/constants.py

@@ -6,13 +6,17 @@ JOB_FAILED = 'failed'
 JOB_ABORTED = 'aborted'
 
 # Nextflow version constants
-AWS_NEXTFLOW_VERSIONS = ['22.10.8', '24.04.4']
+AWS_NEXTFLOW_VERSIONS = ['22.10.8', '24.04.4', '25.04.8', '25.10.4']
 AZURE_NEXTFLOW_VERSIONS = ['22.11.1-edge']
 HPC_NEXTFLOW_VERSIONS = ['22.10.8']
-AWS_NEXTFLOW_LATEST = '24.04.4'
+AWS_NEXTFLOW_LATEST = '25.10.4'
 AZURE_NEXTFLOW_LATEST = '22.11.1-edge'
 HPC_NEXTFLOW_LATEST = '22.10.8'
 
+# Nextflow version defaults by workflow type
+PLATFORM_WORKFLOW_NEXTFLOW_VERSION = '22.10.8'  # For Lifebit Platform workflows (modules)
+USER_WORKFLOW_NEXTFLOW_VERSION = '24.04.4'  # For user-imported workflows
+
 # Job abort states
 ABORT_JOB_STATES = ['running', 'initializing']
 

{cloudos_cli-2.87.1 → cloudos_cli-2.88.1}/cloudos_cli/interactive_session/cli.py

@@ -276,7 +276,8 @@ def list_sessions(ctx,
               help='Cost limit in USD. Default=-1 (unlimited).',
               default=-1)
 @click.option('--shutdown-in',
-              help='Auto-shutdown duration (e.g., 8h, 2d).')
+              help='Auto-shutdown duration (e.g., 8h, 2d). Default=12h.',
+              default='12h')
 @click.option('--mount',
               multiple=True,
               help='Mount a data file into the session. Supports both CloudOS datasets and S3 files. Format: project_name/dataset_path (e.g., leila-test/Data/file.csv) or s3://bucket/path/to/file (e.g., s3://my-bucket/data/file.csv). Can be used multiple times.')
@@ -561,7 +562,8 @@ def create_session(ctx,
             spark_core=spark_core,
             spark_workers=spark_workers,
             data_files=parsed_data_files,
-            s3_mounts=parsed_s3_mounts
+            s3_mounts=parsed_s3_mounts,
+            shutdown_in=shutdown_in
         )
         # Output session link in greppable format for CI/automation
         click.echo(f"Session link: {cloudos_url}/app/data-science/interactive-analysis/view/{session_id}")

{cloudos_cli-2.87.1 → cloudos_cli-2.88.1}/cloudos_cli/interactive_session/interactive_session.py

@@ -1162,7 +1162,7 @@ def build_resume_payload(
 def format_session_creation_table(session_data, instance_type=None, storage_size=None,
                                   backend_type=None, r_version=None,
                                   spark_master=None, spark_core=None, spark_workers=None,
-                                  data_files=None, s3_mounts=None):
+                                  data_files=None, s3_mounts=None, shutdown_in=None):
     """Display session creation result in table format.
 
     Parameters
@@ -1187,6 +1187,8 @@ def format_session_creation_table(session_data, instance_type=None, storage_size
         List of parsed data file objects to display
     s3_mounts : list, optional
         List of parsed S3 mount objects to display
+    shutdown_in : str, optional
+        Shutdown duration value (e.g., '12h', '2d') that was requested
 
     Returns
     -------
@@ -1214,6 +1216,9 @@ def format_session_creation_table(session_data, instance_type=None, storage_size
                        session_data.get('interactiveSessionConfiguration', {}).get('storageSizeInGb')
     storage_display = f"{response_storage} GB" if response_storage else (f"{storage_size} GB" if storage_size else "N/A")
     table.add_row("Storage", storage_display)
+    # Display shutdown duration
+    if shutdown_in:
+        table.add_row("Auto-Shutdown", shutdown_in)
     # Add backend-specific information
     if backend_type == 'rstudio' and r_version:
         table.add_row("R Version", r_version)

{cloudos_cli-2.87.1 → cloudos_cli-2.88.1}/cloudos_cli/jobs/cli.py

@@ -11,6 +11,7 @@ from cloudos_cli.clos import Cloudos
 from cloudos_cli.utils.errors import BadRequestException
 from cloudos_cli.utils.resources import ssl_selector
 from cloudos_cli.utils.details import create_job_details, create_job_list_table
+from cloudos_cli.utils.nextflow_version import resolve_nextflow_version
 from cloudos_cli.cost.cost import CostViewer
 from cloudos_cli.related_analyses.related_analyses import related_analyses
 from cloudos_cli.configure.configure import with_profile_config, CLOUDOS_URL
@@ -18,12 +19,6 @@ from cloudos_cli.link import Link
 from cloudos_cli.constants import (
     JOB_COMPLETED,
     REQUEST_INTERVAL_CROMWELL,
-    AWS_NEXTFLOW_VERSIONS,
-    AZURE_NEXTFLOW_VERSIONS,
-    HPC_NEXTFLOW_VERSIONS,
-    AWS_NEXTFLOW_LATEST,
-    AZURE_NEXTFLOW_LATEST,
-    HPC_NEXTFLOW_LATEST,
     ABORT_JOB_STATES
 )
 import json
@@ -88,9 +83,9 @@ def job():
                     'to use with your job.'))
 @click.option('--nextflow-version',
               help=('Nextflow version to use when executing the workflow in CloudOS. ' +
-                    'Default=22.10.8.'),
-              type=click.Choice(['22.10.8', '24.04.4', '22.11.1-edge', 'latest']),
-              default='22.10.8')
+                    'Defaults to 22.10.8 for Platform Workflows or 24.04.4 for user-imported Workflows.'),
+              type=click.Choice(['22.10.8', '24.04.4', '25.04.8', '25.10.4', '22.11.1-edge', 'latest']),
+              default=None)
 @click.option('--git-commit',
               help=('The git commit hash to run for ' +
                     'the selected pipeline. ' +
@@ -298,6 +293,16 @@ def run(ctx,
     cl = Cloudos(cloudos_url, apikey, cromwell_token)
     workflow_type = cl.detect_workflow(workflow_name, workspace_id, verify_ssl, last)
     is_module = cl.is_module(workflow_name, workspace_id, verify_ssl, last)
+    
+    # Resolve and validate Nextflow version
+    nextflow_version = resolve_nextflow_version(
+        nextflow_version=nextflow_version,
+        execution_platform=execution_platform,
+        is_module=is_module,
+        workflow_name=workflow_name,
+        verbose=verbose
+    )
+    
     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.')
@@ -348,13 +353,8 @@ def run(ctx,
                   f'Platform Workflow "{workflow_name}". Platform Workflows ' +
                   'use their own predetermined queues.')
         job_queue_id = None
-        if nextflow_version != '22.10.8':
-            print(f'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'
         if execution_platform == 'azure':
-            print(f'The selected worflow \'{workflow_name}\' ' +
+            print(f'The selected workflow \'{workflow_name}\' ' +
                   'is a CloudOS module. For these workflows, worker nodes ' +
                   'are managed internally. For this reason, the options ' +
                   'azure-worker-instance-type, azure-worker-instance-disk and ' +
@@ -382,33 +382,7 @@ def run(ctx,
             docker_login = True
     else:
         docker_login = False
-    if nextflow_version == 'latest':
-        if execution_platform == 'aws':
-            nextflow_version = AWS_NEXTFLOW_LATEST
-        elif execution_platform == 'azure':
-            nextflow_version = AZURE_NEXTFLOW_LATEST
-        else:
-            nextflow_version = HPC_NEXTFLOW_LATEST
-        print('You have specified Nextflow version \'latest\' for execution platform ' +
-              f'\'{execution_platform}\'. The workflow will use the ' +
-              f'latest version available on CloudOS: {nextflow_version}.')
-    if execution_platform == 'aws':
-        if nextflow_version not in AWS_NEXTFLOW_VERSIONS:
-            print('For execution platform \'aws\', the workflow will use the default ' +
-                  '\'22.10.8\' version on CloudOS.')
-            nextflow_version = '22.10.8'
-    if execution_platform == 'azure':
-        if nextflow_version not in AZURE_NEXTFLOW_VERSIONS:
-            print('For execution platform \'azure\', the workflow will use the \'22.11.1-edge\' ' +
-                  'version on CloudOS.')
-            nextflow_version = '22.11.1-edge'
-    if execution_platform == 'hpc':
-        if nextflow_version not in HPC_NEXTFLOW_VERSIONS:
-            print('For execution platform \'hpc\', the workflow will use the \'22.10.8\' version on CloudOS.')
-            nextflow_version = '22.10.8'
-    if nextflow_version != '22.10.8' and nextflow_version != '22.11.1-edge':
-        click.secho(f'You have specified Nextflow version {nextflow_version}. This version requires the pipeline ' +
-              'to be written in DSL2 and does not support DSL1.', fg='yellow', bold=True)
+    
     print('\nExecuting run...')
     if workflow_type == 'nextflow':
         print(f'\tNextflow version: {nextflow_version}')
@@ -1737,9 +1711,8 @@ def archive_unarchive_jobs(ctx,
               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. ' +
-                    'Default=22.10.8.'),
-              type=click.Choice(['22.10.8', '24.04.4', '22.11.1-edge', 'latest']))
+              help=('Nextflow version to use when executing the workflow in CloudOS.'),
+              type=click.Choice(['22.10.8', '24.04.4', '25.04.8', '25.10.4', '22.11.1-edge', 'latest']))
 @click.option('--git-branch',
               help=('The branch to run for the selected pipeline. ' +
                     'If not specified it defaults to the last commit ' +

cloudos_cli-2.88.1/cloudos_cli/utils/nextflow_version.py

@@ -0,0 +1,128 @@
+"""Nextflow version resolution and validation utilities."""
+
+import rich_click as click
+from cloudos_cli.constants import (
+    AWS_NEXTFLOW_VERSIONS,
+    AZURE_NEXTFLOW_VERSIONS,
+    HPC_NEXTFLOW_VERSIONS,
+    AWS_NEXTFLOW_LATEST,
+    AZURE_NEXTFLOW_LATEST,
+    HPC_NEXTFLOW_LATEST,
+    PLATFORM_WORKFLOW_NEXTFLOW_VERSION,
+    USER_WORKFLOW_NEXTFLOW_VERSION
+)
+
+
+def resolve_nextflow_version(
+    nextflow_version,
+    execution_platform,
+    is_module,
+    workflow_name=None,
+    verbose=False
+):
+    """
+    Resolve and validate the Nextflow version for a job submission.
+    
+    This function handles:
+    - Dynamic defaults based on execution platform and workflow type
+    - 'latest' version resolution
+    - Platform workflow version forcing
+    - Platform-specific version validation with appropriate warnings/errors
+    
+    Args:
+        nextflow_version (str or None): The requested Nextflow version, or None for default
+        execution_platform (str): The execution platform ('aws', 'azure', or 'hpc')
+        is_module (bool): Whether the workflow is a Platform workflow (module)
+        workflow_name (str, optional): The workflow name for informative messages
+        verbose (bool, optional): Whether to print verbose messages
+    
+    Returns:
+        str: The resolved and validated Nextflow version
+    
+    Raises:
+        click.BadParameter: If an unsupported version is specified for AWS or HPC platforms
+    """
+    
+    # Step 1: Set dynamic default if no version specified
+    if nextflow_version is None:
+        if execution_platform == 'azure':
+            nextflow_version = AZURE_NEXTFLOW_LATEST  # Azure has fixed Nextflow version
+            if verbose:
+                print(f'\t...Using default Nextflow version {AZURE_NEXTFLOW_LATEST} for Azure')
+        elif execution_platform == 'hpc':
+            nextflow_version = HPC_NEXTFLOW_LATEST  # HPC has fixed Nextflow version
+            if verbose:
+                print(f'\t...Using default Nextflow version {HPC_NEXTFLOW_LATEST} for HPC')
+        elif is_module:
+            nextflow_version = PLATFORM_WORKFLOW_NEXTFLOW_VERSION  # Lifebit Platform workflows (AWS)
+            if verbose:
+                print(f'\t...Using default Nextflow version {PLATFORM_WORKFLOW_NEXTFLOW_VERSION} for Platform Workflow')
+        else:
+            nextflow_version = USER_WORKFLOW_NEXTFLOW_VERSION  # User-imported workflows (AWS only)
+            if verbose:
+                print(f'\t...Using default Nextflow version {USER_WORKFLOW_NEXTFLOW_VERSION} for user-imported workflow')
+    
+    # Step 2: Resolve 'latest' to actual version
+    if nextflow_version == 'latest':
+        if execution_platform == 'aws':
+            nextflow_version = AWS_NEXTFLOW_LATEST
+        elif execution_platform == 'azure':
+            nextflow_version = AZURE_NEXTFLOW_LATEST
+        else:
+            nextflow_version = HPC_NEXTFLOW_LATEST
+        print('You have specified Nextflow version \'latest\' for execution platform ' +
+              f'\'{execution_platform}\'. The workflow will use the ' +
+              f'latest version available on CloudOS: {nextflow_version}.')
+    
+    # Step 3: Force correct version for Platform workflows
+    if is_module:
+        if execution_platform == 'azure':
+            if nextflow_version != AZURE_NEXTFLOW_LATEST:
+                workflow_msg = f' \'{workflow_name}\'' if workflow_name else ''
+                print(f'The selected workflow{workflow_msg} ' +
+                      'is a CloudOS Platform Workflow on Azure. Platform Workflows on Azure only work with ' +
+                      f'Nextflow version {AZURE_NEXTFLOW_LATEST}. Switching to use {AZURE_NEXTFLOW_LATEST}')
+            nextflow_version = AZURE_NEXTFLOW_LATEST
+        else:
+            if nextflow_version != PLATFORM_WORKFLOW_NEXTFLOW_VERSION:
+                workflow_msg = f' \'{workflow_name}\'' if workflow_name else ''
+                print(f'The selected workflow{workflow_msg} ' +
+                      'is a CloudOS Platform Workflow. Platform Workflows only work with ' +
+                      f'Nextflow version {PLATFORM_WORKFLOW_NEXTFLOW_VERSION}. Switching to use {PLATFORM_WORKFLOW_NEXTFLOW_VERSION}')
+            nextflow_version = PLATFORM_WORKFLOW_NEXTFLOW_VERSION
+    
+    # Step 4: Validate version for execution platform
+    if execution_platform == 'aws':
+        if nextflow_version not in AWS_NEXTFLOW_VERSIONS:
+            available_versions = ', '.join(AWS_NEXTFLOW_VERSIONS)
+            raise click.BadParameter(
+                f'Unsupported Nextflow version \'{nextflow_version}\' for AWS execution platform. '
+                f'Supported versions are: {available_versions}.'
+            )
+    elif execution_platform == 'azure':
+        if nextflow_version not in AZURE_NEXTFLOW_VERSIONS:
+            available_versions = ', '.join(AZURE_NEXTFLOW_VERSIONS)
+            click.secho(
+                f'Warning: Nextflow version \'{nextflow_version}\' is not supported for Azure execution platform. '
+                f'Azure only supports: {available_versions}. Switching to use {AZURE_NEXTFLOW_LATEST}.',
+                fg='yellow', bold=True
+            )
+            nextflow_version = AZURE_NEXTFLOW_LATEST
+    elif execution_platform == 'hpc':
+        if nextflow_version not in HPC_NEXTFLOW_VERSIONS:
+            available_versions = ', '.join(HPC_NEXTFLOW_VERSIONS)
+            raise click.BadParameter(
+                f'Unsupported Nextflow version \'{nextflow_version}\' for HPC execution platform. '
+                f'HPC only supports: {available_versions}.'
+            )
+    
+    # Step 5: Warn about DSL2 requirement for newer versions
+    legacy_versions = [PLATFORM_WORKFLOW_NEXTFLOW_VERSION, AZURE_NEXTFLOW_LATEST]
+    if nextflow_version not in legacy_versions:
+        click.secho(
+            f'The Nextflow version being used is: {nextflow_version}. This version requires the pipeline ' +
+            'to be written in DSL2 and does not support DSL1.',
+            fg='yellow', bold=True
+        )
+    
+    return nextflow_version

{cloudos_cli-2.87.1 → cloudos_cli-2.88.1}/cloudos_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.87.1
+Version: 2.88.1
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -687,6 +687,29 @@ When there are duplicate `--workflow-name` in the platform, you can add the `--l
 
 _For example, the pipeline `lifebit-process` was imported on May 23 2025 and again on May 30 2025; with the `--last` flag, it will use the import of May 30, 2025._
 
+**Nextflow Version Support**
+
+CloudOS CLI supports multiple Nextflow versions, with intelligent defaults based on your workflow type and execution platform.
+
+**Default Version Behavior:**
+
+The default Nextflow version is automatically selected based on your workflow type and execution platform:
+
+- **Azure Platform**: Always uses `22.11.1-edge` regardless of workflow type
+- **Platform Workflows** (AWS/HPC): Uses `22.10.8` (Lifebit provided workflows and modules)
+- **User-Imported Workflows** (AWS/HPC): AWS uses `24.04.4`; HPC uses `22.10.8`
+
+**Specifying a Custom Version:**
+
+You can override the default by using the `--nextflow-version` parameter:
+
+```bash
+cloudos job run --profile my_profile --workflow-name rnatoy --job-config cloudos_cli/examples/rnatoy.config --nextflow-version 25.04.8 --resumable
+```
+
+> [!NOTE]
+> **Azure Platform Behavior**: If you specify a Nextflow version not supported by Azure (anything other than 22.11.1-edge), CloudOS CLI will display a warning and automatically use 22.11.1-edge instead. Your job will proceed without error.
+
 **AWS Executor Support**
 
 CloudOS supports [AWS batch](https://www.nextflow.io/docs/latest/executor.html?highlight=executors#aws-batch) executor by default.
@@ -705,6 +728,7 @@ cloudos job run --profile my_profile --workflow-name rnatoy --job-config cloudos
 CloudOS can also be configured to use Microsoft Azure compute platforms. If your CloudOS is configured to use Azure, you will need to take into consideration the following:
 
 - When sending jobs to CloudOS using `cloudos job run` command, please use the option `--execution-platform azure`
+- Azure only supports Nextflow version `22.11.1-edge`. If you specify a different version, CloudOS CLI will display a warning and automatically use `22.11.1-edge` instead
 - Due to the lack of AWS batch queues in Azure, `cloudos queue list` command is not working
 
 Other than that, `cloudos-cli` will work very similarly. For instance, this is a typical send job command:
@@ -2154,7 +2178,7 @@ cloudos interactive-session create \
 - `--spot`: Use spot instances (AWS only, cost-saving)
 - `--shared`: Make session accessible to workspace members
 - `--cost-limit`: Compute cost limit in USD (default: -1 for unlimited)
-- `--shutdown-in`: Auto-shutdown duration (e.g., `8h`, `2d`, `30m`)
+- `--shutdown-in`: Auto-shutdown duration (e.g., `8h`, `2d`, `30m`, default: `12h`)
 
 **Data & Storage Management:**
 - `--mount`: Mount a data file into the session. Supports both CloudOS datasets and S3 files (AWS only). Format: `project_name/dataset_path` (e.g., `leila-test/Data/file.csv`) or `s3://bucket/path/to/file` (e.g., `s3://my-bucket/data/file.csv`). Can be used multiple times.

{cloudos_cli-2.87.1 → cloudos_cli-2.88.1}/cloudos_cli.egg-info/SOURCES.txt

@@ -54,6 +54,7 @@ cloudos_cli/utils/cloud.py
 cloudos_cli/utils/details.py
 cloudos_cli/utils/errors.py
 cloudos_cli/utils/last_wf.py
+cloudos_cli/utils/nextflow_version.py
 cloudos_cli/utils/requests.py
 cloudos_cli/utils/resources.py
 cloudos_cli/workflows/__init__.py
@@ -62,6 +63,7 @@ tests/__init__.py
 tests/functions_for_pytest.py
 tests/test_cli_project_create.py
 tests/test_error_messages.py
+tests/test_nextflow_version.py
 tests/test_cost/__init__.py
 tests/test_cost/test_job_cost.py
 tests/test_interactive_session/__init__.py

cloudos_cli-2.88.1/tests/test_nextflow_version.py

@@ -0,0 +1,177 @@
+"""Tests for Nextflow version resolution utilities."""
+
+import pytest
+import rich_click as click
+from unittest.mock import patch
+from cloudos_cli.utils.nextflow_version import resolve_nextflow_version
+from cloudos_cli.constants import (
+    AWS_NEXTFLOW_LATEST,
+    AZURE_NEXTFLOW_LATEST,
+    HPC_NEXTFLOW_LATEST,
+    PLATFORM_WORKFLOW_NEXTFLOW_VERSION,
+    USER_WORKFLOW_NEXTFLOW_VERSION,
+    AWS_NEXTFLOW_VERSIONS
+)
+
+
+class TestResolveNextflowVersion:
+    """Test cases for resolve_nextflow_version function."""
+    
+    def test_default_azure_version(self):
+        """Test that Azure always defaults to AZURE_NEXTFLOW_LATEST."""
+        result = resolve_nextflow_version(
+            nextflow_version=None,
+            execution_platform='azure',
+            is_module=False
+        )
+        assert result == AZURE_NEXTFLOW_LATEST
+    
+    def test_default_hpc_version(self):
+        """Test that HPC always defaults to HPC_NEXTFLOW_LATEST."""
+        result = resolve_nextflow_version(
+            nextflow_version=None,
+            execution_platform='hpc',
+            is_module=False
+        )
+        assert result == HPC_NEXTFLOW_LATEST
+    
+    def test_default_aws_platform_workflow(self):
+        """Test that AWS Platform workflows default to PLATFORM_WORKFLOW_NEXTFLOW_VERSION."""
+        result = resolve_nextflow_version(
+            nextflow_version=None,
+            execution_platform='aws',
+            is_module=True
+        )
+        assert result == PLATFORM_WORKFLOW_NEXTFLOW_VERSION
+    
+    def test_default_aws_user_workflow(self):
+        """Test that AWS user-imported workflows default to USER_WORKFLOW_NEXTFLOW_VERSION."""
+        result = resolve_nextflow_version(
+            nextflow_version=None,
+            execution_platform='aws',
+            is_module=False
+        )
+        assert result == USER_WORKFLOW_NEXTFLOW_VERSION
+    
+    def test_latest_resolution_aws(self):
+        """Test that 'latest' resolves to AWS_NEXTFLOW_LATEST."""
+        result = resolve_nextflow_version(
+            nextflow_version='latest',
+            execution_platform='aws',
+            is_module=False
+        )
+        assert result == AWS_NEXTFLOW_LATEST
+    
+    def test_latest_resolution_azure(self):
+        """Test that 'latest' resolves to AZURE_NEXTFLOW_LATEST."""
+        result = resolve_nextflow_version(
+            nextflow_version='latest',
+            execution_platform='azure',
+            is_module=False
+        )
+        assert result == AZURE_NEXTFLOW_LATEST
+    
+    def test_latest_resolution_hpc(self):
+        """Test that 'latest' resolves to HPC_NEXTFLOW_LATEST."""
+        result = resolve_nextflow_version(
+            nextflow_version='latest',
+            execution_platform='hpc',
+            is_module=False
+        )
+        assert result == HPC_NEXTFLOW_LATEST
+    
+    def test_platform_workflow_forces_azure_version(self):
+        """Test that Platform workflows on Azure are forced to AZURE_NEXTFLOW_LATEST."""
+        result = resolve_nextflow_version(
+            nextflow_version='24.04.4',  # User tries different version
+            execution_platform='azure',
+            is_module=True,
+            workflow_name='test-workflow'
+        )
+        assert result == AZURE_NEXTFLOW_LATEST
+    
+    def test_platform_workflow_forces_aws_version(self):
+        """Test that Platform workflows on AWS are forced to PLATFORM_WORKFLOW_NEXTFLOW_VERSION."""
+        result = resolve_nextflow_version(
+            nextflow_version='24.04.4',  # User tries different version
+            execution_platform='aws',
+            is_module=True,
+            workflow_name='test-workflow'
+        )
+        assert result == PLATFORM_WORKFLOW_NEXTFLOW_VERSION
+    
+    def test_valid_aws_version_accepted(self):
+        """Test that valid AWS versions are accepted."""
+        for version in AWS_NEXTFLOW_VERSIONS:
+            result = resolve_nextflow_version(
+                nextflow_version=version,
+                execution_platform='aws',
+                is_module=False
+            )
+            assert result == version
+    
+    def test_invalid_aws_version_raises_error(self):
+        """Test that invalid AWS version raises BadParameter."""
+        with pytest.raises(click.BadParameter, match='Unsupported Nextflow version'):
+            resolve_nextflow_version(
+                nextflow_version='99.99.99',
+                execution_platform='aws',
+                is_module=False
+            )
+    
+    def test_invalid_hpc_version_raises_error(self):
+        """Test that invalid HPC version raises BadParameter."""
+        with pytest.raises(click.BadParameter, match='Unsupported Nextflow version'):
+            resolve_nextflow_version(
+                nextflow_version='24.04.4',  # Not supported on HPC
+                execution_platform='hpc',
+                is_module=False
+            )
+    
+    def test_azure_invalid_version_auto_corrects(self):
+        """Test that Azure auto-corrects invalid versions with warning."""
+        with patch('cloudos_cli.utils.nextflow_version.click.secho') as mock_secho:
+            result = resolve_nextflow_version(
+                nextflow_version='24.04.4',  # Not supported on Azure
+                execution_platform='azure',
+                is_module=False
+            )
+            assert result == AZURE_NEXTFLOW_LATEST
+            # Verify warning was displayed
+            mock_secho.assert_called_once()
+            assert 'Warning' in mock_secho.call_args[0][0]
+    
+    def test_verbose_output(self, capsys):
+        """Test that verbose flag produces output."""
+        resolve_nextflow_version(
+            nextflow_version=None,
+            execution_platform='aws',
+            is_module=True,
+            verbose=True
+        )
+        captured = capsys.readouterr()
+        assert 'Using default Nextflow version' in captured.out
+    
+    def test_dsl2_warning_for_new_versions(self):
+        """Test that DSL2 warning is displayed for newer versions."""
+        with patch('cloudos_cli.utils.nextflow_version.click.secho') as mock_secho:
+            resolve_nextflow_version(
+                nextflow_version=USER_WORKFLOW_NEXTFLOW_VERSION,
+                execution_platform='aws',
+                is_module=False
+            )
+            # Should have warning about DSL2
+            mock_secho.assert_called_once()
+            assert 'DSL2' in mock_secho.call_args[0][0]
+    
+    def test_no_dsl2_warning_for_legacy_versions(self):
+        """Test that no DSL2 warning for legacy versions."""
+        with patch('cloudos_cli.utils.nextflow_version.click.secho') as mock_secho:
+            resolve_nextflow_version(
+                nextflow_version=PLATFORM_WORKFLOW_NEXTFLOW_VERSION,
+                execution_platform='aws',
+                is_module=False
+            )
+            # Should not have any warnings
+            mock_secho.assert_not_called()
+

cloudos_cli-2.87.1/cloudos_cli/_version.py

@@ -1 +0,0 @@
-__version__ = '2.87.1'