Docker API version mismatch in devcontainer

[camlloyd]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

I have forked nf-core/modules and opened this in GitHub Codespaces.

When I try to run nf-core modules test <module>, it fails with the following error:

Command error:                                                                                                                                    
     docker: Error response from daemon: client version 1.52 is too new. Maximum supported API version is 1.43                                       
                                                                                                                                                     
     Run 'docker run --help' for more information    

The change proposed in nextflow-io/training@ce7ddbc fixes this for me.

Thanks goes to @vdauwera for pointing me in the right direction. I am happy to submit a PR.

Command used and terminal output

nf-core modules test <module>

Relevant files

No response

System information

No response

[camlloyd]

Example below:

Details

/workspaces/modules -> nf-core modules test fastqdl


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\ 
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.6.0.dev0 - https://nf-co.re


? Choose container software to run the test with Docker
INFO     Generating nf-test snapshot                                                                                                                   
╭────────────────────────────────────────────────────────────────── nf-test output ───────────────────────────────────────────────────────────────────╮
│                                                                                                                                                     │
│ 🚀 nf-test 0.9.3                                                                                                                                    │
│ https://www.nf-test.com                                                                                                                             │
│ (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr                                                                                                │
│                                                                                                                                                     │
│ Load .nf-test/plugins/nft-anndata/0.1.0/nft-anndata-0.1.0.jar                                                                                       │
│ Load .nf-test/plugins/nft-bam/0.6.0/nft-bam-0.6.0.jar                                                                                               │
│ Load .nf-test/plugins/nft-csv/0.1.0/nft-csv-0.1.0.jar                                                                                               │
│ Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar                                                                                     │
│ Load .nf-test/plugins/nft-fastq/0.0.1/nft-fastq-0.0.1.jar                                                                                           │
│ Load .nf-test/plugins/nft-utils/0.0.7/nft-utils-0.0.7.jar                                                                                           │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar                                                                                               │
│                                                                                                                                                     │
│ Test Process FASTQDL                                                                                                                                │
│                                                                                                                                                     │
│   Test [56127c5a] 'fastqdl - run' FAILED (5.271s)                                                                                                   │
│                                                                                                                                                     │
│   Assertion failed:                                                                                                                                 │
│                                                                                                                                                     │
│   2 of 2 assertions failed                                                                                                                          │
│                                                                                                                                                     │
│   Nextflow stdout:                                                                                                                                  │
│                                                                                                                                                     │
│   ERROR ~ Error executing process > 'FASTQDL (test)'                                                                                                │
│                                                                                                                                                     │
│   Caused by:                                                                                                                                        │
│     Process `FASTQDL (test)` terminated with an error exit status (125)                                                                             │
│                                                                                                                                                     │
│                                                                                                                                                     │
│   Command executed:                                                                                                                                 │
│                                                                                                                                                     │
│     fastq-dl \                                                                                                                                      │
│          \                                                                                                                                          │
│         --prefix test \                                                                                                                             │
│         --accession ERR5069949 \                                                                                                                    │
│         --cpus 2 \                                                                                                                                  │
│         --outdir .                                                                                                                                  │
│                                                                                                                                                     │
│     cat <<-END_VERSIONS > versions.yml                                                                                                              │
│     "FASTQDL":                                                                                                                                      │
│         fastq-dl: $(fastq-dl --version |& sed 's/.* //')                                                                                            │
│     END_VERSIONS                                                                                                                                    │
│                                                                                                                                                     │
│   Command exit status:                                                                                                                              │
│     125                                                                                                                                             │
│                                                                                                                                                     │
│   Command output:                                                                                                                                   │
│     (empty)                                                                                                                                         │
│                                                                                                                                                     │
│   Command error:                                                                                                                                    │
│     docker: Error response from daemon: client version 1.52 is too new. Maximum supported API version is 1.43                                       │
│                                                                                                                                                     │
│     Run 'docker run --help' for more information                                                                                                    │
│                                                                                                                                                     │
│   Work dir:                                                                                                                                         │
│     /workspaces/modules/.nf-test/tests/56127c5adeae5f32e289ff7f2310a42f/work/2e/c5426675e792420199d429ce4fc2a9                                      │
│                                                                                                                                                     │
│   Container:                                                                                                                                        │
│     quay.io/biocontainers/fastq-dl:3.0.1--pyhdfd78af_0                                                                                              │
│                                                                                                                                                     │
│   Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`                   │
│                                                                                                                                                     │
│    -- Check '/workspaces/modules/.nf-test/tests/56127c5adeae5f32e289ff7f2310a42f/meta/nextflow.log' file for details                                │
│   Nextflow stderr:                                                                                                                                  │
│                                                                                                                                                     │
│                                                                                                                                                     │
│                                                                                                                                                     │
│   Test [30235821] 'fastqdl - experiment' FAILED (5.751s)                                                                                            │
│                                                                                                                                                     │
│   Assertion failed:                                                                                                                                 │
│                                                                                                                                                     │
│   2 of 2 assertions failed                                                                                                                          │
│                                                                                                                                                     │
│   Nextflow stdout:                                                                                                                                  │
│                                                                                                                                                     │
│   ERROR ~ Error executing process > 'FASTQDL (test)'                                                                                                │
│                                                                                                                                                     │
│   Caused by:                                                                                                                                        │
│     Process `FASTQDL (test)` terminated with an error exit status (125)                                                                             │
│                                                                                                                                                     │
│                                                                                                                                                     │
│   Command executed:                                                                                                                                 │
│                                                                                                                                                     │
│     fastq-dl \                                                                                                                                      │
│          \                                                                                                                                          │
│         --prefix test \                                                                                                                             │
│         --accession ERX4876079 \                                                                                                                    │
│         --cpus 2 \                                                                                                                                  │
│         --outdir .                                                                                                                                  │
│                                                                                                                                                     │
│     cat <<-END_VERSIONS > versions.yml                                                                                                              │
│     "FASTQDL":                                                                                                                                      │
│         fastq-dl: $(fastq-dl --version |& sed 's/.* //')                                                                                            │
│     END_VERSIONS                                                                                                                                    │
│                                                                                                                                                     │
│   Command exit status:                                                                                                                              │
│     125                                                                                                                                             │
│                                                                                                                                                     │
│   Command output:                                                                                                                                   │
│     (empty)                                                                                                                                         │
│                                                                                                                                                     │
│   Command error:                                                                                                                                    │
│     docker: Error response from daemon: client version 1.52 is too new. Maximum supported API version is 1.43                                       │
│                                                                                                                                                     │
│     Run 'docker run --help' for more information                                                                                                    │
│                                                                                                                                                     │
│   Work dir:                                                                                                                                         │
│     /workspaces/modules/.nf-test/tests/3023582108b95ab46805b5e816d89b35/work/55/c9964f6398107ad074a988f1792ad0                                      │
│                                                                                                                                                     │
│   Container:                                                                                                                                        │
│     quay.io/biocontainers/fastq-dl:3.0.1--pyhdfd78af_0                                                                                              │
│                                                                                                                                                     │
│   Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`                   │
│                                                                                                                                                     │
│    -- Check '/workspaces/modules/.nf-test/tests/3023582108b95ab46805b5e816d89b35/meta/nextflow.log' file for details                                │
│   Nextflow stderr:                                                                                                                                  │
│                                                                                                                                                     │
│                                                                                                                                                     │
│                                                                                                                                                     │
│   Test [42acb7fb] 'fastqdl - run - stub' FAILED (5.932s)                                                                                            │
│                                                                                                                                                     │
│   Assertion failed:                                                                                                                                 │
│                                                                                                                                                     │
│   2 of 2 assertions failed                                                                                                                          │
│                                                                                                                                                     │
│   Nextflow stdout:                                                                                                                                  │
│                                                                                                                                                     │
│   ERROR ~ Error executing process > 'FASTQDL (test)'                                                                                                │
│                                                                                                                                                     │
│   Caused by:                                                                                                                                        │
│     Process `FASTQDL (test)` terminated with an error exit status (125)                                                                             │
│                                                                                                                                                     │
│                                                                                                                                                     │
│   Command executed:                                                                                                                                 │
│                                                                                                                                                     │
│     echo "" | gzip > ERR5069949.fastq.gz                                                                                                            │
│     echo "" | gzip > ERR5069949_1.fastq.gz                                                                                                          │
│     echo "" | gzip > ERR5069949_2.fastq.gz                                                                                                          │
│     touch test-run-info.tsv                                                                                                                         │
│                                                                                                                                                     │
│     cat <<-END_VERSIONS > versions.yml                                                                                                              │
│     "FASTQDL":                                                                                                                                      │
│         fastq-dl: $(fastq-dl --version |& sed 's/.* //')                                                                                            │
│     END_VERSIONS                                                                                                                                    │
│                                                                                                                                                     │
│   Command exit status:                                                                                                                              │
│     125                                                                                                                                             │
│                                                                                                                                                     │
│   Command output:                                                                                                                                   │
│     (empty)                                                                                                                                         │
│                                                                                                                                                     │
│   Command error:                                                                                                                                    │
│     docker: Error response from daemon: client version 1.52 is too new. Maximum supported API version is 1.43                                       │
│                                                                                                                                                     │
│     Run 'docker run --help' for more information                                                                                                    │
│                                                                                                                                                     │
│   Work dir:                                                                                                                                         │
│     /workspaces/modules/.nf-test/tests/42acb7fb2dc74a208edf5028d5bdae94/work/74/ed83b999d9386d0f2d6836ae0e5ce3                                      │
│                                                                                                                                                     │
│   Container:                                                                                                                                        │
│     quay.io/biocontainers/fastq-dl:3.0.1--pyhdfd78af_0                                                                                              │
│                                                                                                                                                     │
│   Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line                           │
│                                                                                                                                                     │
│    -- Check '/workspaces/modules/.nf-test/tests/42acb7fb2dc74a208edf5028d5bdae94/meta/nextflow.log' file for details                                │
│   Nextflow stderr:                                                                                                                                  │
│                                                                                                                                                     │
│                                                                                                                                                     │
│                                                                                                                                                     │
│   Test [c3611d8f] 'fastqdl - experiment - stub' FAILED (5.764s)                                                                                     │
│                                                                                                                                                     │
│   Assertion failed:                                                                                                                                 │
│                                                                                                                                                     │
│   2 of 2 assertions failed                                                                                                                          │
│                                                                                                                                                     │
│   Nextflow stdout:                                                                                                                                  │
│                                                                                                                                                     │
│   ERROR ~ Error executing process > 'FASTQDL (test)'                                                                                                │
│                                                                                                                                                     │
│   Caused by:                                                                                                                                        │
│     Process `FASTQDL (test)` terminated with an error exit status (125)                                                                             │
│                                                                                                                                                     │
│                                                                                                                                                     │
│   Command executed:                                                                                                                                 │
│                                                                                                                                                     │
│     echo "" | gzip > ERX4876079.fastq.gz                                                                                                            │
│     echo "" | gzip > ERX4876079_1.fastq.gz                                                                                                          │
│     echo "" | gzip > ERX4876079_2.fastq.gz                                                                                                          │
│     touch test-run-info.tsv                                                                                                                         │
│                                                                                                                                                     │
│     cat <<-END_VERSIONS > versions.yml                                                                                                              │
│     "FASTQDL":                                                                                                                                      │
│         fastq-dl: $(fastq-dl --version |& sed 's/.* //')                                                                                            │
│     END_VERSIONS                                                                                                                                    │
│                                                                                                                                                     │
│   Command exit status:                                                                                                                              │
│     125                                                                                                                                             │
│                                                                                                                                                     │
│   Command output:                                                                                                                                   │
│     (empty)                                                                                                                                         │
│                                                                                                                                                     │
│   Command error:                                                                                                                                    │
│     docker: Error response from daemon: client version 1.52 is too new. Maximum supported API version is 1.43                                       │
│                                                                                                                                                     │
│     Run 'docker run --help' for more information                                                                                                    │
│                                                                                                                                                     │
│   Work dir:                                                                                                                                         │
│     /workspaces/modules/.nf-test/tests/c3611d8f9db04895e4b5f559588c1d2/work/0d/bd6c1747ef4a45054da7a1981c3091                                       │
│                                                                                                                                                     │
│   Container:                                                                                                                                        │
│     quay.io/biocontainers/fastq-dl:3.0.1--pyhdfd78af_0                                                                                              │
│                                                                                                                                                     │
│   Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line                           │
│                                                                                                                                                     │
│    -- Check '/workspaces/modules/.nf-test/tests/c3611d8f9db04895e4b5f559588c1d2/meta/nextflow.log' file for details                                 │
│   Nextflow stderr:                                                                                                                                  │
│                                                                                                                                                     │
│                                                                                                                                                     │
│                                                                                                                                                     │
│     Obsolete snapshots can only be checked if all tests of a file are executed successful.                                                          │
│                                                                                                                                                     │
│                                                                                                                                                     │
│ FAILURE: Executed 4 tests in 22.751s (4 failed)                                                                                                     │
│                                                                                                                                                     │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─────────────────────────────────────────────────────────────────── nf-test error ───────────────────────────────────────────────────────────────────╮
│ Assertion failed:                                                                                                                                   │
│                                                                                                                                                     │
│ assert process.success                                                                                                                              │
│        |       |                                                                                                                                    │
│        FASTQDL false                                                                                                                                │
│                                                                                                                                                     │
│ java.lang.RuntimeException: Different Snapshot:                                                                                                     │
│ --- /tmp/expected2374434965789665098jso +++ /tmp/found7036347465142107439json                                                         │
│ n                                                                                                                                      │
│ @@ -1,56 @@                             @@ +1,28 @@                                                                                   │
│    1 [                                     1 [                                                                                                      │
│    2     {                                 2     {                                                                                                  │
│    3         "0": [                        3         "0": [                                                                                         │
│ !  4             [                      !  4                                                                               │
│ -  5                 {                                                                                                            │
│ -  6                     "id": "test"                                                                                             │
│ -  7                 },                                                                                                           │
│ -  8                 [                                                                                                            │
│ -  9                     "ERR5069949.fa                                                                                           │
│ stq.gz:md5,c931a862c2126788432684cca99d                                                                                        │
│ b416",                                                                                                                      │
│ - 10                     "ERR5069949_1.                                                                                           │
│ fastq.gz:md5,b643cdf5f6a8fae5063fb2b7c1                                                                                        │
│ 72071d",                                                                                                                    │
│ - 11                     "ERR5069949_2.                                                                                           │
│ fastq.gz:md5,685c1b66d8bf0c20a37402a057                                                                                        │
│ 8acca2"                                                                                                                     │
│ - 12                 ]                                                                                                            │
│ - 13             ]                                                                                                                │
│   14         ],                            5         ],                                                                                             │
│   15         "1": [                        6         "1": [                                                                                         │
│ ! 16             [                      !  7                                                                               │
│ - 17                 {                                                                                                            │
│ - 18                     "id": "test"                                                                                             │
│ - 19                 },                                                                                                           │
│ - 20                 "test-run-info.tsv                                                                                           │
│ :md5,b24c159ce9c90cde9e0397df11377cb6"                                                                                      │
│ - 21             ]                                                                                                                │
│   22         ],                            8         ],                                                                                             │
│   23         "2": [                        9         "2": [                                                                                         │
│   24                                      10                                                                                                        │
│   25         ],                           11         ],                                                                                             │
│   26         "3": [                       12         "3": [                                                                                         │
│ ! 27             "versions.yml:md5,1c78 ! 13                                                                    │
│ c47d16f00ad96065c7a4830e89e0"                                                                                               │
│   28         ],                           14         ],                                                                                             │
│   29         "fastq": [                   15         "fastq": [                                                                                     │
│ ! 30             [                      ! 16                                                                               │
│ - 31                 {                                                                                                            │
│ - 32                     "id": "test"                                                                                             │
│ - 33                 },                                                                                                           │
│ - 34                 [                                                                                                            │
│ - 35                     "ERR5069949.fa                                                                                           │
│ stq.gz:md5,c931a862c2126788432684cca99d                                                                                        │
│ b416",                                                                                                                      │
│ - 36                     "ERR5069949_1.                                                                                           │
│ fastq.gz:md5,b643cdf5f6a8fae5063fb2b7c1                                                                                        │
│ 72071d",                                                                                                                    │
│ - 37                     "ERR5069949_2.                                                                                           │
│ fastq.gz:md5,685c1b66d8bf0c20a37402a057                                                                                        │
│ 8acca2"                                                                                                                     │
│ - 38                 ]                                                                                                            │
│ - 39             ]                                                                                                                │
│   40         ],                           17         ],                                                                                             │
│   41         "runinfo": [                 18         "runinfo": [                                                                                   │
│ ! 42             [                      ! 19                                                                               │
│ - 43                 {                                                                                                            │
│ - 44                     "id": "test"                                                                                             │
│ - 45                 },                                                                                                           │
│ - 46                 "test-run-info.tsv                                                                                           │
│ :md5,b24c159ce9c90cde9e0397df11377cb6"                                                                                      │
│ - 47             ]                                                                                                                │
│   48         ],                           20         ],                                                                                             │
│   49         "runmergers": [              21         "runmergers": [                                                                                │
│   50                                      22                                                                                                        │
│   51         ],                           23         ],                                                                                             │
│   52         "versions": [                24         "versions": [                                                                                  │
│ ! 53             "versions.yml:md5,1c78 ! 25                                                                    │
│ c47d16f00ad96065c7a4830e89e0"                                                                                               │
│   54         ]                            26         ]                                                                                              │
│   55     }                                27     }                                                                                                  │
│   56 ]                                    28 ]                                                                                                      │
│                                                                                                                                                     │
│ Assertion failed:                                                                                                                                   │
│                                                                                                                                                     │
│ assert process.success                                                                                                                              │
│        |       |                                                                                                                                    │
│        FASTQDL false                                                                                                                                │
│                                                                                                                                                     │
│ java.lang.RuntimeException: Different Snapshot:                                                                                                     │
│ --- /tmp/expected15879562628233258547js +++ /tmp/found17152196267289126274json                                                        │
│ on                                                                                                                                     │
│ @@ -1,56 @@                             @@ +1,28 @@                                                                                   │
│    1 [                                     1 [                                                                                                      │
│    2     {                                 2     {                                                                                                  │
│    3         "0": [                        3         "0": [                                                                                         │
│ !  4             [                      !  4                                                                               │
│ -  5                 {                                                                                                            │
│ -  6                     "id": "test"                                                                                             │
│ -  7                 },                                                                                                           │
│ -  8                 [                                                                                                            │
│ -  9                     "ERR5069949.fa                                                                                           │
│ stq.gz:md5,c931a862c2126788432684cca99d                                                                                        │
│ b416",                                                                                                                      │
│ - 10                     "ERR5069949_1.                                                                                           │
│ fastq.gz:md5,b643cdf5f6a8fae5063fb2b7c1                                                                                        │
│ 72071d",                                                                                                                    │
│ - 11                     "ERR5069949_2.                                                                                           │
│ fastq.gz:md5,685c1b66d8bf0c20a37402a057                                                                                        │
│ 8acca2"                                                                                                                     │
│ - 12                 ]                                                                                                            │
│ - 13             ]                                                                                                                │
│   14         ],                            5         ],                                                                                             │
│   15         "1": [                        6         "1": [                                                                                         │
│ ! 16             [                      !  7                                                                               │
│ - 17                 {                                                                                                            │
│ - 18                     "id": "test"                                                                                             │
│ - 19                 },                                                                                                           │
│ - 20                 "test-run-info.tsv                                                                                           │
│ :md5,b24c159ce9c90cde9e0397df11377cb6"                                                                                      │
│ - 21             ]                                                                                                                │
│   22         ],                            8         ],                                                                                             │
│   23         "2": [                        9         "2": [                                                                                         │
│   24                                      10                                                                                                        │
│   25         ],                           11         ],                                                                                             │
│   26         "3": [                       12         "3": [                                                                                         │
│ ! 27             "versions.yml:md5,1c78 ! 13                                                                    │
│ c47d16f00ad96065c7a4830e89e0"                                                                                               │
│   28         ],                           14         ],                                                                                             │
│   29         "fastq": [                   15         "fastq": [                                                                                     │
│ ! 30             [                      ! 16                                                                               │
│ - 31                 {                                                                                                            │
│ - 32                     "id": "test"                                                                                             │
│ - 33                 },                                                                                                           │
│ - 34                 [                                                                                                            │
│ - 35                     "ERR5069949.fa                                                                                           │
│ stq.gz:md5,c931a862c2126788432684cca99d                                                                                        │
│ b416",                                                                                                                      │
│ - 36                     "ERR5069949_1.                                                                                           │
│ fastq.gz:md5,b643cdf5f6a8fae5063fb2b7c1                                                                                        │
│ 72071d",                                                                                                                    │
│ - 37                     "ERR5069949_2.                                                                                           │
│ fastq.gz:md5,685c1b66d8bf0c20a37402a057                                                                                        │
│ 8acca2"                                                                                                                     │
│ - 38                 ]                                                                                                            │
│ - 39             ]                                                                                                                │
│   40         ],                           17         ],                                                                                             │
│   41         "runinfo": [                 18         "runinfo": [                                                                                   │
│ ! 42             [                      ! 19                                                                               │
│ - 43                 {                                                                                                            │
│ - 44                     "id": "test"                                                                                             │
│ - 45                 },                                                                                                           │
│ - 46                 "test-run-info.tsv                                                                                           │
│ :md5,b24c159ce9c90cde9e0397df11377cb6"                                                                                      │
│ - 47             ]                                                                                                                │
│   48         ],                           20         ],                                                                                             │
│   49         "runmergers": [              21         "runmergers": [                                                                                │
│   50                                      22                                                                                                        │
│   51         ],                           23         ],                                                                                             │
│   52         "versions": [                24         "versions": [                                                                                  │
│ ! 53             "versions.yml:md5,1c78 ! 25                                                                    │
│ c47d16f00ad96065c7a4830e89e0"                                                                                               │
│   54         ]                            26         ]                                                                                              │
│   55     }                                27     }                                                                                                  │
│   56 ]                                    28 ]                                                                                                      │
│                                                                                                                                                     │
│ Assertion failed:                                                                                                                                   │
│                                                                                                                                                     │
│ assert process.success                                                                                                                              │
│        |       |                                                                                                                                    │
│        FASTQDL false                                                                                                                                │
│                                                                                                                                                     │
│ java.lang.RuntimeException: Different Snapshot:                                                                                                     │
│ --- /tmp/expected204430805570145818json +++ /tmp/found12825281804740858643json                                                        │
│ @@ -1,56 @@                             @@ +1,28 @@                                                                                   │
│    1 [                                     1 [                                                                                                      │
│    2     {                                 2     {                                                                                                  │
│    3         "0": [                        3         "0": [                                                                                         │
│ !  4             [                      !  4                                                                               │
│ -  5                 {                                                                                                            │
│ -  6                     "id": "test"                                                                                             │
│ -  7                 },                                                                                                           │
│ -  8                 [                                                                                                            │
│ -  9                     "ERR5069949.fa                                                                                           │
│ stq.gz:md5,68b329da9893e34099c7d8ad5cb9                                                                                        │
│ c940",                                                                                                                      │
│ - 10                     "ERR5069949_1.                                                                                           │
│ fastq.gz:md5,68b329da9893e34099c7d8ad5c                                                                                        │
│ b9c940",                                                                                                                    │
│ - 11                     "ERR5069949_2.                                                                                           │
│ fastq.gz:md5,68b329da9893e34099c7d8ad5c                                                                                        │
│ b9c940"                                                                                                                     │
│ - 12                 ]                                                                                                            │
│ - 13             ]                                                                                                                │
│   14         ],                            5         ],                                                                                             │
│   15         "1": [                        6         "1": [                                                                                         │
│ ! 16             [                      !  7                                                                               │
│ - 17                 {                                                                                                            │
│ - 18                     "id": "test"                                                                                             │
│ - 19                 },                                                                                                           │
│ - 20                 "test-run-info.tsv                                                                                           │
│ :md5,d41d8cd98f00b204e9800998ecf8427e"                                                                                      │
│ - 21             ]                                                                                                                │
│   22         ],                            8         ],                                                                                             │
│   23         "2": [                        9         "2": [                                                                                         │
│   24                                      10                                                                                                        │
│   25         ],                           11         ],                                                                                             │
│   26         "3": [                       12         "3": [                                                                                         │
│ ! 27             "versions.yml:md5,1c78 ! 13                                                                    │
│ c47d16f00ad96065c7a4830e89e0"                                                                                               │
│   28         ],                           14         ],                                                                                             │
│   29         "fastq": [                   15         "fastq": [                                                                                     │
│ ! 30             [                      ! 16                                                                               │
│ - 31                 {                                                                                                            │
│ - 32                     "id": "test"                                                                                             │
│ - 33                 },                                                                                                           │
│ - 34                 [                                                                                                            │
│ - 35                     "ERR5069949.fa                                                                                           │
│ stq.gz:md5,68b329da9893e34099c7d8ad5cb9                                                                                        │
│ c940",                                                                                                                      │
│ - 36                     "ERR5069949_1.                                                                                           │
│ fastq.gz:md5,68b329da9893e34099c7d8ad5c                                                                                        │
│ b9c940",                                                                                                                    │
│ - 37                     "ERR5069949_2.                                                                                           │
│ fastq.gz:md5,68b329da9893e34099c7d8ad5c                                                                                        │
│ b9c940"                                                                                                                     │
│ - 38                 ]                                                                                                            │
│ - 39             ]                                                                                                                │
│   40         ],                           17         ],                                                                                             │
│   41         "runinfo": [                 18         "runinfo": [                                                                                   │
│ ! 42             [                      ! 19                                                                               │
│ - 43                 {                                                                                                            │
│ - 44                     "id": "test"                                                                                             │
│ - 45                 },                                                                                                           │
│ - 46                 "test-run-info.tsv                                                                                           │
│ :md5,d41d8cd98f00b204e9800998ecf8427e"                                                                                      │
│ - 47             ]                                                                                                                │
│   48         ],                           20         ],                                                                                             │
│   49         "runmergers": [              21         "runmergers": [                                                                                │
│   50                                      22                                                                                                        │
│   51         ],                           23         ],                                                                                             │
│   52         "versions": [                24         "versions": [                                                                                  │
│ ! 53             "versions.yml:md5,1c78 ! 25                                                                    │
│ c47d16f00ad96065c7a4830e89e0"                                                                                               │
│   54         ]                            26         ]                                                                                              │
│   55     }                                27     }                                                                                                  │
│   56 ]                                    28 ]                                                                                                      │
│                                                                                                                                                     │
│ Assertion failed:                                                                                                                                   │
│                                                                                                                                                     │
│ assert process.success                                                                                                                              │
│        |       |                                                                                                                                    │
│        FASTQDL false                                                                                                                                │
│                                                                                                                                                     │
│ java.lang.RuntimeException: Different Snapshot:                                                                                                     │
│ --- /tmp/expected4103192316533896478jso +++ /tmp/found11051883171693535918json                                                        │
│ n                                                                                                                                      │
│ @@ -1,56 @@                             @@ +1,28 @@                                                                                   │
│    1 [                                     1 [                                                                                                      │
│    2     {                                 2     {                                                                                                  │
│    3         "0": [                        3         "0": [                                                                                         │
│ !  4             [                      !  4                                                                               │
│ -  5                 {                                                                                                            │
│ -  6                     "id": "test"                                                                                             │
│ -  7                 },                                                                                                           │
│ -  8                 [                                                                                                            │
│ -  9                     "ERX4876079.fa                                                                                           │
│ stq.gz:md5,68b329da9893e34099c7d8ad5cb9                                                                                        │
│ c940",                                                                                                                      │
│ - 10                     "ERX4876079_1.                                                                                           │
│ fastq.gz:md5,68b329da9893e34099c7d8ad5c                                                                                        │
│ b9c940",                                                                                                                    │
│ - 11                     "ERX4876079_2.                                                                                           │
│ fastq.gz:md5,68b329da9893e34099c7d8ad5c                                                                                        │
│ b9c940"                                                                                                                     │
│ - 12                 ]                                                                                                            │
│ - 13             ]                                                                                                                │
│   14         ],                            5         ],                                                                                             │
│   15         "1": [                        6         "1": [                                                                                         │
│ ! 16             [                      !  7                                                                               │
│ - 17                 {                                                                                                            │
│ - 18                     "id": "test"                                                                                             │
│ - 19                 },                                                                                                           │
│ - 20                 "test-run-info.tsv                                                                                           │
│ :md5,d41d8cd98f00b204e9800998ecf8427e"                                                                                      │
│ - 21             ]                                                                                                                │
│   22         ],                            8         ],                                                                                             │
│   23         "2": [                        9         "2": [                                                                                         │
│   24                                      10                                                                                                        │
│   25         ],                           11         ],                                                                                             │
│   26         "3": [                       12         "3": [                                                                                         │
│ ! 27             "versions.yml:md5,1c78 ! 13                                                                    │
│ c47d16f00ad96065c7a4830e89e0"                                                                                               │
│   28         ],                           14         ],                                                                                             │
│   29         "fastq": [                   15         "fastq": [                                                                                     │
│ ! 30             [                      ! 16                                                                               │
│ - 31                 {                                                                                                            │
│ - 32                     "id": "test"                                                                                             │
│ - 33                 },                                                                                                           │
│ - 34                 [                                                                                                            │
│ - 35                     "ERX4876079.fa                                                                                           │
│ stq.gz:md5,68b329da9893e34099c7d8ad5cb9                                                                                        │
│ c940",                                                                                                                      │
│ - 36                     "ERX4876079_1.                                                                                           │
│ fastq.gz:md5,68b329da9893e34099c7d8ad5c                                                                                        │
│ b9c940",                                                                                                                    │
│ - 37                     "ERX4876079_2.                                                                                           │
│ fastq.gz:md5,68b329da9893e34099c7d8ad5c                                                                                        │
│ b9c940"                                                                                                                     │
│ - 38                 ]                                                                                                            │
│ - 39             ]                                                                                                                │
│   40         ],                           17         ],                                                                                             │
│   41         "runinfo": [                 18         "runinfo": [                                                                                   │
│ ! 42             [                      ! 19                                                                               │
│ - 43                 {                                                                                                            │
│ - 44                     "id": "test"                                                                                             │
│ - 45                 },                                                                                                           │
│ - 46                 "test-run-info.tsv                                                                                           │
│ :md5,d41d8cd98f00b204e9800998ecf8427e"                                                                                      │
│ - 47             ]                                                                                                                │
│   48         ],                           20         ],                                                                                             │
│   49         "runmergers": [              21         "runmergers": [                                                                                │
│   50                                      22                                                                                                        │
│   51         ],                           23         ],                                                                                             │
│   52         "versions": [                24         "versions": [                                                                                  │
│ ! 53             "versions.yml:md5,1c78 ! 25                                                                    │
│ c47d16f00ad96065c7a4830e89e0"                                                                                               │
│   54         ]                            26         ]                                                                                              │
│   55     }                                27     }                                                                                                  │
│   56 ]                                    28 ]                                                                                                      │
│                                                                                                                                                     │
│                                                                                                                                                     │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
ERROR    nf-test failed due to differences in the snapshots                                                                                            
INFO     All tests passed!                                                                                                                             
/workspaces/modules -> 

[vdauwera]

Thanks for reporting this! I've flagged it to the infrastructure team on Slack.

[JulianFlesch]

We are running a "docker-outside-of-docker" setup here: When trying to run a docker command inside the devcontainer, the docker cli is talking to the deamon running on the host machine (outside the devcontainer).

For your specific issue there is a quick fix: you can ask the docker client inside devcontainer to use an older api version.

export DOCKER_API_VERSION=1.43

I'll investigate if this is also useful as a general solution for the modules devcontainer

[JulianFlesch]

Draft PR for reference to solve this for your setup: #9921

[camlloyd]

Thanks!