module update: subread/featurecounts - Bump container versions #10249

[PeterKneale]

The container image version needs to be updated
nf-co.re/modules/subread_featurecounts

from:
https://depot.galaxyproject.org/singularity/subread/2.0.6--he4a0461_2
biocontainers/subread:2.0.6--he4a0461_2

to:
https://depot.galaxyproject.org/singularity/subread/2.1.1--h577a1d6_0
biocontainers/subread:2.1.1--h577a1d6_0

Tests run in both docker and singularity.

PR checklist

Closes #10249

• This comment contains a description of changes (with reason).
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda

[PeterKneale]

prettier...................................................................................Passed
trim trailing whitespace...................................................................Passed
fix end of files...........................................................................Passed
Match meta.ymls in one of the subdirectories of modules/nf-core............................Passed
Validate environment.ymls against schema...............................(no files to check)Skipped
Match meta.ymls in one of the subdirectories of subworkflows/nf-core.......................Passed
Validate GitHub Workflows..............................................(no files to check)Skipped
ruff (legacy alias)....................................................(no files to check)Skipped
ruff format............................................................(no files to check)Skipped
Lint Dockerfiles.......................................................(no files to check)Skipped
[bump_subread_featurecounts_version 61b27d3b3] module update: subread/featurecounts - Bump container versions #10249
 19 files changed, 44 insertions(+), 110 deletions(-)

[PeterKneale]

All tests pass

nf-core module test subread/featurecounts --profile singularity --no-prompts
INFO     Generating nf-test snapshot                                                                                                                                                                                               
INFO     All tests passed!                                                                             

nf-core module test subread/featurecounts --profile conda --no-prompts
INFO     Generating nf-test snapshot                                                                                                                                                                                               
INFO     Generating nf-test snapshot again to check stability                                                                                                                                                                      
INFO     All tests passed!  

nf-core module test subread/featurecounts --profile docker --no-prompts
INFO     Generating nf-test snapshot                                                                                                                                                                                               
INFO     All tests passed!                             

[awgymer]

I don't think you have added the changed snapshots into this PR. At the very least I would expect the versions output to have changed (I'd be concerned if it hadn't) but it also seems that some of the actual outputs are showing different md5sum too. I don't know this tool so I cannot really say whether those changes are correct/expected given the version bump.

[SPPearce]

You need to run nf-core modules test subread/featurecounts -u to update the test snapshots.
You also need to update the environment.yml file, which controls the conda installation as well.

[PeterKneale]

/workspaces/modules -> nf-core modules test subread/featurecounts -u


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

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


? Choose container software to run the test with Conda
INFO     Generating nf-test snapshot                                                                                                                           
Displaying nf-test output
╭────────────────────────────────────────────────────────────────────── nf-test output ───────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                             │
│ 🚀 nf-test 0.9.4                                                                                                                                            │
│ 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/0.1.0/nft-fastq-0.1.0.jar                                                                                                   │
│ Load .nf-test/plugins/nft-utils/0.0.9/nft-utils-0.0.9.jar                                                                                                   │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar                                                                                                       │
│ Warning: every snapshot that fails during this test run is re-recorded.                                                                                     │
│                                                                                                                                                             │
│ Test Process SUBREAD_FEATURECOUNTS                                                                                                                          │
│                                                                                                                                                             │
│   Test [96bc0ffc] 'sarscov2 [bam] - forward' PASSED (32.766s)                                                                                               │
│   Test [85e65198] 'sarscov2 [bam] - forward - stub' PASSED (25.081s)                                                                                        │
│   Test [2c31840b] 'sarscov2 [bam] - reverse' PASSED (21.564s)                                                                                               │
│   Test [c83b2e7f] 'sarscov2 [bam] - reverse - stub' PASSED (22.78s)                                                                                         │
│   Test [c3193d11] 'sarscov2 [bam] - unstranded' PASSED (21.174s)                                                                                            │
│   Test [a3e6a9a0] 'sarscov2 [bam] - unstranded - stub' PASSED (22.858s)                                                                                     │
│                                                                                                                                                             │
│                                                                                                                                                             │
│ SUCCESS: Executed 6 tests in 146.231s                                                                                                                       │
│                                                                                                                                                             │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Displaying nf-test error 
INFO     Generating nf-test snapshot again to check stability                                                                                                  
Displaying nf-test output
╭────────────────────────────────────────────────────────────────────── nf-test output ───────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                             │
│ 🚀 nf-test 0.9.4                                                                                                                                            │
│ 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/0.1.0/nft-fastq-0.1.0.jar                                                                                                   │
│ Load .nf-test/plugins/nft-utils/0.0.9/nft-utils-0.0.9.jar                                                                                                   │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar                                                                                                       │
│                                                                                                                                                             │
│ Test Process SUBREAD_FEATURECOUNTS                                                                                                                          │
│                                                                                                                                                             │
│   Test [96bc0ffc] 'sarscov2 [bam] - forward' PASSED (21.696s)                                                                                               │
│   Test [85e65198] 'sarscov2 [bam] - forward - stub' PASSED (20.499s)                                                                                        │
│   Test [2c31840b] 'sarscov2 [bam] - reverse' PASSED (21.781s)                                                                                               │
│   Test [c83b2e7f] 'sarscov2 [bam] - reverse - stub' PASSED (20.881s)                                                                                        │
│   Test [c3193d11] 'sarscov2 [bam] - unstranded' PASSED (21.967s)                                                                                            │
│   Test [a3e6a9a0] 'sarscov2 [bam] - unstranded - stub' PASSED (20.778s)                                                                                     │
│                                                                                                                                                             │
│                                                                                                                                                             │
│ SUCCESS: Executed 6 tests in 127.724s                                                                                                                       │
│                                                                                                                                                             │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Displaying nf-test error 
CRITICAL Ran, but found errors:                                                                                                                                
          - nf-test failed                                                                                                                                     
          - nf-test failed    

[PeterKneale]

@SPPearce I've updated per your instructions, the output from nf-test looks slightly contradictory. Curious to see the results when they run as part of the CI.

[SPPearce]

Is it expected that the featureCounts tsv file is changing?

[PeterKneale]

No, i dont believe so