Hi all How do I set up the dev containers we were talking ab nf-core #cellpainting

Hi all! How do I set up the dev containers we were...

Kate B

09/08/2025, 3:52 PM

Hi all! How do I set up the dev containers we were talking about last week? I'm trying to run

nf-test test modules/local/cellprofiler/assaydevelopment/

and it's failing with

cellprofiler: command not found

and my guess is that it's a container/environment issue? During the meeting I had tried to follow along but my VSCode looked different than the example. Thanks!

Ken Brewer

09/10/2025, 7:05 PM

Don't forget to add

--profile docker

to your nf-test command. That's what tells it to use docker when running the tests so it can find cellprofiler.

Kate B

09/10/2025, 7:08 PM

Got it, I used

--profile podman

because I don't have a Docker license and I no longer got the command not found error, but it fails because of different snapshots?

Kate B

09/10/2025, 7:09 PM

Copy code

(base) wm4ff-0f9:cellpainting kbowers$ nf-test test modules/local/cellprofiler/assaydevelopment/ --profile podman

🚀 nf-test 0.9.2
<https://www.nf-test.com>
(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr

Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar
Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar

Test Process CELLPROFILER_ASSAYDEVELOPMENT

  Test [7b500f9e] 'cellprofiler - assay development' 
java.lang.RuntimeException: Different Snapshot:
[										[
    {										    {
        "0": [									        "0": [
            									   |	            [
										   >	                {
										   >	                    "id": "2021_04_26_Batch1_BR00117035_A01",
										   >	                    "batch": "2021_04_26_Batch1",
										   >	                    "plate": "BR00117035",
										   >	                    "well": "A01"
										   >	                },
										   >	                "2021_04_26_Batch1_BR00117035_A01_ObjectOverlay.png:md5,6deadaad0c7a4f8fd2739ee5
										   >	            ]
        ],									        ],
        "1": [									        "1": [
            									            
        ],									        ],
        "2": [									        "2": [
            									   |	            "versions.yml:md5,766f4a17b8a2ba2a5e108b7f5fee144e"
        ],									        ],
        "csv": [								        "csv": [
            									            
        ],									        ],
        "png": [								        "png": [
            									   |	            [
										   >	                {
										   >	                    "id": "2021_04_26_Batch1_BR00117035_A01",
										   >	                    "batch": "2021_04_26_Batch1",
										   >	                    "plate": "BR00117035",
										   >	                    "well": "A01"
										   >	                },
										   >	                "2021_04_26_Batch1_BR00117035_A01_ObjectOverlay.png:md5,6deadaad0c7a4f8fd2739ee5
										   >	            ]
        ],									        ],
        "versions": [								        "versions": [
            									   |	            "versions.yml:md5,766f4a17b8a2ba2a5e108b7f5fee144e"
        ]									        ]
    }										    }
]
\ No newline at end of file
										]
\ No newline at end of file


FAILED (41.834s)

  Assertion failed: 
  
  1 of 2 assertions failed
  
  Nextflow stdout:
  
  Nextflow stderr:
  
  Nextflow 25.04.7 is available - Please consider updating your version to it
  

  Test [9db0db06] 'cellprofiler - assay development - stub' java.lang.RuntimeException: Different Snapshot:
[													[
    {													    {
        "0": [												        "0": [
            [												            [
                {											                {
                    "id": "2021_04_26_Batch1_BR00117035_A01",						                    "id": "2021_04_26_Batch1_BR00117035_A01",
                    "batch": "2021_04_26_Batch1",							                    "batch": "2021_04_26_Batch1",
                    "plate": "BR00117035",								                    "plate": "BR00117035",
                    "well": "A01"									                    "well": "A01"
                },											                },
                "mock_segmentedimage.png:md5,b01821571f44eb5a12bf2a145ac96a3e"				                "mock_segmentedimage.png:md5,b01821571f44eb5a12bf2a145ac96a3e"
            ]												            ]
        ],												        ],
        "1": [												        "1": [
            												            
        ],												        ],
        "2": [												        "2": [
            "versions.yml:md5,f5804f9e60c58eb106e7bcd78cfc0d19"					   |	            "versions.yml:md5,766f4a17b8a2ba2a5e108b7f5fee144e"
        ],												        ],
        "csv": [											        "csv": [
            												            
        ],												        ],
        "png": [											        "png": [
            [												            [
                {											                {
                    "id": "2021_04_26_Batch1_BR00117035_A01",						                    "id": "2021_04_26_Batch1_BR00117035_A01",
                    "batch": "2021_04_26_Batch1",							                    "batch": "2021_04_26_Batch1",
                    "plate": "BR00117035",								                    "plate": "BR00117035",
                    "well": "A01"									                    "well": "A01"
                },											                },
                "mock_segmentedimage.png:md5,b01821571f44eb5a12bf2a145ac96a3e"				                "mock_segmentedimage.png:md5,b01821571f44eb5a12bf2a145ac96a3e"
            ]												            ]
        ],												        ],
        "versions": [											        "versions": [
            "versions.yml:md5,f5804f9e60c58eb106e7bcd78cfc0d19"					   |	            "versions.yml:md5,766f4a17b8a2ba2a5e108b7f5fee144e"
        ]												        ]
    }													    }
]
\ No newline at end of file
													]
\ No newline at end of file


FAILED (12.199s)

  Assertion failed: 
  
  1 of 2 assertions failed
  
  Nextflow stdout:
  
  Nextflow stderr:
  
  Nextflow 25.04.7 is available - Please consider updating your version to it
  

    Obsolete snapshots can only be checked if all tests of a file are executed successful.


FAILURE: Executed 2 tests in 54.074s (2 failed)

Ken Brewer

09/11/2025, 2:23 PM

@Kate B This might be a situation where you need to update the snapshot https://www.nf-test.com/docs/assertions/snapshots/ https://training.nextflow.io/latest/side_quests/nf-test/#2-test-a-nextflow-process

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