Feat: Adds support for new nextflow versions and changes version defaults

.github/workflows/ci.yml

@@ -244,7 +244,7 @@ jobs:
         INSTANCE_TYPE: "m4.xlarge"
       run: |
         JOB_NAME="$JOB_NAME_BASE""|GitHubCommit:""${COMMIT_HASH:0:6}""|PR-NUMBER:""$PR_NUMBER"
-        cloudos job run --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --project-name "$PROJECT_NAME" --workflow-name "$WORKFLOW" --job-config $JOB_CONFIG --job-name "$JOB_NAME" --wait-completion --resumable --instance-type $INSTANCE_TYPE 2>&1 | tee out.txt
+        cloudos job run --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --project-name "$PROJECT_NAME" --workflow-name "$WORKFLOW" --nextflow-version 22.10.8 --job-config $JOB_CONFIG --job-name "$JOB_NAME" --wait-completion --resumable --instance-type $INSTANCE_TYPE 2>&1 | tee out.txt
         JOB_ID=$(grep -e "Your assigned job id is:" out.txt | rev | cut -f1 -d " " | rev)
         echo "job_id=$JOB_ID" >> $GITHUB_OUTPUT
         cloudos job status --cloudos-url $CLOUDOS_URL --workspace-id $CLOUDOS_WORKSPACE_ID --apikey $CLOUDOS_TOKEN --job-id $JOB_ID
@@ -800,7 +800,7 @@ jobs:
       run: |
         # Step 1: Run job (without --wait-completion so it doesn't wait until completion)
         JOB_NAME="$JOB_NAME_BASE""|GitHubCommit:""${COMMIT_HASH:0:6}""|PR-NUMBER:""$PR_NUMBER"
-        cloudos job run --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --project-name "$PROJECT_NAME" --workflow-name "$WORKFLOW" --job-config $JOB_CONFIG --job-name "$JOB_NAME" --instance-type $INSTANCE_TYPE 2>&1 | tee out.txt
+        cloudos job run --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --project-name "$PROJECT_NAME" --workflow-name "$WORKFLOW" --nextflow-version 22.10.8 --job-config $JOB_CONFIG --job-name "$JOB_NAME" --instance-type $INSTANCE_TYPE 2>&1 | tee out.txt
         JOB_ID=$(grep -e "Your assigned job id is:" out.txt | rev | cut -f1 -d " " | rev)
         echo "Job ID: $JOB_ID"
 
@@ -893,6 +893,7 @@ jobs:
             --workspace-id $CLOUDOS_WORKSPACE_ID \
             --project-name "$PROJECT_NAME" \
             --workflow-name "$WORKFLOW" \
+            --nextflow-version 22.10.8 \
             --job-name "$JOB_NAME_BASE|GitHubCommit:${COMMIT_HASH:0:6}|PR-NUMBER:$PR_NUMBER" \
             --instance-type m4.xlarge \
             --params-file "$PARAMS_FILE" \

.github/workflows/ci_az.yml

@@ -36,7 +36,7 @@ jobs:
         CLOUDOS_WORKSPACE_ID: ${{ secrets.CLOUDOS_WORKSPACE_ID_AZURE }}
         CLOUDOS_URL: "https://dev.sdlc.lifebit.ai"
       run: |
-        cloudos job list --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID
+        echo q | cloudos job list --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID
   job_list_filtering_az:
     needs: job_run_and_status_az
     runs-on: ubuntu-latest
@@ -62,15 +62,15 @@ jobs:
       run: |
         JOB_ID="${{ needs.job_run_and_status_az.outputs.job_id }}"
         # Test filtering by status, project  and workflow name
-        cloudos job list --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --filter-status completed --filter-project cloudos-cli-tests  --filter-workflow GH-rnatoy --last --last-n-jobs 10
+        echo q | cloudos job list --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --filter-status completed --filter-project cloudos-cli-tests  --filter-workflow GH-rnatoy --last --last-n-jobs 10
         # Test filtering job id
-        cloudos job list --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --filter-job-id $JOB_ID 
+        echo q | cloudos job list --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --filter-job-id $JOB_ID 
         # Test filtering job name
-        cloudos job list --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --filter-job-name "cloudos-cli-CI-test" --last-n-jobs 10
+        echo q | cloudos job list --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --filter-job-name "cloudos-cli-CI-test" --last-n-jobs 10
         # Test filtering by only mine
-        cloudos job list --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --filter-only-mine --last-n-jobs 10
+        echo q | cloudos job list --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --filter-only-mine --last-n-jobs 10
         # Test filtering by queue
-        #cloudos job list --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --filter-queue "cost_saving_standard_nextflow" --last-n-jobs 10
+        #echo q | cloudos job list --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --filter-queue "cost_saving_standard_nextflow" --last-n-jobs 10
   job_details_az:
     needs: job_run_and_status_az
     runs-on: ubuntu-latest

.github/workflows/ci_dev.yml

@@ -225,7 +225,7 @@ jobs:
         INSTANCE_TYPE: "m4.xlarge"
       run: |
         JOB_NAME="$JOB_NAME_BASE""|GitHubCommit:""${COMMIT_HASH:0:6}""|PR-NUMBER:""$PR_NUMBER"
-        cloudos job run --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --project-name "$PROJECT_NAME" --workflow-name "$WORKFLOW" --job-config $JOB_CONFIG --job-name "$JOB_NAME" --wait-completion --resumable --instance-type $INSTANCE_TYPE 2>&1 | tee out.txt
+        cloudos job run --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --project-name "$PROJECT_NAME" --workflow-name "$WORKFLOW" --nextflow-version 22.10.8 --job-config $JOB_CONFIG --job-name "$JOB_NAME" --wait-completion --resumable --instance-type $INSTANCE_TYPE 2>&1 | tee out.txt
         JOB_ID=$(grep -e "Your assigned job id is:" out.txt | rev | cut -f1 -d " " | rev)
         echo "job_id=$JOB_ID" >> $GITHUB_OUTPUT
         cloudos job status --cloudos-url $CLOUDOS_URL --workspace-id $CLOUDOS_WORKSPACE_ID --apikey $CLOUDOS_TOKEN --job-id $JOB_ID
@@ -782,7 +782,7 @@ jobs:
       run: |
         # Step 1: Run job (without --wait-completion so it doesn't wait until completion)
         JOB_NAME="$JOB_NAME_BASE""|GitHubCommit:""${COMMIT_HASH:0:6}""|PR-NUMBER:""$PR_NUMBER"
-        cloudos job run --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --project-name "$PROJECT_NAME" --workflow-name "$WORKFLOW" --job-config $JOB_CONFIG --job-name "$JOB_NAME" --instance-type $INSTANCE_TYPE 2>&1 | tee out.txt
+        cloudos job run --cloudos-url $CLOUDOS_URL --apikey $CLOUDOS_TOKEN --workspace-id $CLOUDOS_WORKSPACE_ID --project-name "$PROJECT_NAME" --workflow-name "$WORKFLOW" --nextflow-version 22.10.8 --job-config $JOB_CONFIG --job-name "$JOB_NAME" --instance-type $INSTANCE_TYPE 2>&1 | tee out.txt
         JOB_ID=$(grep -e "Your assigned job id is:" out.txt | rev | cut -f1 -d " " | rev)
         echo "Job ID: $JOB_ID"
 
@@ -899,6 +899,7 @@ jobs:
             --workspace-id $CLOUDOS_WORKSPACE_ID \
             --project-name "$PROJECT_NAME" \
             --workflow-name "$WORKFLOW" \
+            --nextflow-version 22.10.8 \
             --job-name "$JOB_NAME_BASE|GitHubCommit:${COMMIT_HASH:0:6}|PR-NUMBER:$PR_NUMBER" \
             --instance-type m4.xlarge \
             --params-file "$PARAMS_FILE" \

CHANGELOG.md

@@ -1,5 +1,12 @@
 ## lifebit-ai/cloudos-cli: changelog
 
+## v2.88.0 (2026-04-03)
+
+### Feat
+
+- Adds support for nextflow versions '25.04.8' and '25.10.4'
+- Updates nextflow versions defaults for user imported pipelines and lifebit-owned pipelines
+
 ## v2.86.0 (2026-03-23)
 
 ### Feat

README.md

@@ -646,6 +646,29 @@ 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): Uses `24.04.4`
+
+**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.
@@ -664,6 +687,7 @@ 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:

cloudos_cli/_version.py

@@ -1 +1 @@
-__version__ = '2.86.0'
+__version__ = '2.88.0'

cloudos_cli/constants.py

@@ -6,10 +6,10 @@
 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'
 

cloudos_cli/jobs/cli.py

@@ -83,9 +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. ' +
@@ -293,6 +293,26 @@ 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)
+
+    # Set dynamic default for Nextflow version based on execution platform and workflow type
+    if nextflow_version is None:
+        if execution_platform == 'azure':
+            nextflow_version = '22.11.1-edge'  # Azure has fixed Nextflow version
+            if verbose:
+                print('\t...Using default Nextflow version 22.11.1-edge for Azure')
+        elif execution_platform == 'hpc':
+            nextflow_version = '22.10.8'  # HPC has fixed Nextflow version
+            if verbose:
+                print('\t...Using default Nextflow version 22.10.8 for HPC')
+        elif is_module:
+            nextflow_version = '22.10.8'  # Lifebit Platform workflows (AWS)
+            if verbose:
+                print('\t...Using default Nextflow version 22.10.8 for Platform Workflow')
+        else:
+            nextflow_version = '24.04.4'  # User-imported workflows (AWS only)
+            if verbose:
+                print('\t...Using default Nextflow version 24.04.4 for user-imported workflow')
+
     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.')
@@ -343,11 +363,19 @@ 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'
+        # Platform workflows have fixed Nextflow versions per execution platform
+        if execution_platform == 'azure':
+            if nextflow_version != '22.11.1-edge':
+                print(f'The selected workflow \'{workflow_name}\' ' +
+                      'is a CloudOS Platform Workflow on Azure. Platform Workflows on Azure only work with ' +
+                      'Nextflow version 22.11.1-edge. Switching to use 22.11.1-edge')
+            nextflow_version = '22.11.1-edge'
+        else:
+            if nextflow_version != '22.10.8':
+                print(f'The selected workflow \'{workflow_name}\' ' +
+                      'is a CloudOS Platform Workflow. Platform Workflows 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}\' ' +
                   'is a CloudOS module. For these workflows, worker nodes ' +
@@ -389,19 +417,28 @@ def run(ctx,
               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'
+            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}.'
+            )
     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'
+            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
     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':
+            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}.'
+            )
+    if nextflow_version not in ['22.10.8', '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...')
@@ -1704,7 +1741,7 @@ def archive_unarchive_jobs(ctx,
 @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']))
+              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 ' +