update to new versions capture for checkm2 databasedownload and checkm2 predict by eit-maxlcummins · Pull Request #9744 · nf-core/modules

eit-maxlcummins · 2026-01-22T13:15:10Z

Updating checkm2 modules to migrate versions to topic channels.

Also fixed a bug with checkm2/databasedownload that causes zenodo to block the user agent model and causes tests to fail. Tests fail even with main branch.

PR checklist

…m2 predict

mashehu · 2026-01-23T10:03:05Z

modules/nf-core/checkm2/databasedownload/tests/main.nf.test

            assertAll(
                { assert process.success },
-                { assert snapshot(process.out.versions).match() },
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() },


Any specific reason why process.out.database is not captured?

Local dev now captures database via this assertion:

{ assert path(process.out.database.get(0).get(1)).exists() },

Unable to snapshot the file as its 16gb.

Open to other suggestions re assertions for the database

Once tests pass and snapshots are updated for this and other subworkflows/module setups which use checkm2 I will update the PR

…--user-agent and jobs fail

eit-maxlcummins · 2026-01-30T09:45:43Z

An update - Ongoing dev required here - Zenodo now blocks CheckM2 database downloads via aria2c default --user-agent. Seems to happen inconsistently, but often attempts to download are met with status 403

  01/29 22:03:15 [[1;32mNOTICE[0m] Downloading 1 item(s)
  
  01/29 22:03:16 [[1;31mERROR[0m] CUID#7 - Download aborted. URI=https://zenodo.org/records/14897628/files/checkm2_database.tar.gz
  Exception: [AbstractCommand.cc:351] errorCode=22 URI=https://zenodo.org/records/14897628/files/checkm2_database.tar.gz
    -> [HttpSkipResponseCommand.cc:239] errorCode=22 The response status is not successful. status=403

Hope to get this wrapped up today but it has been a bit of a process

mashehu · 2026-01-30T09:50:51Z

how big is the data? can it be added to https://github.com/nf-core/test-datasets/ ?

eit-maxlcummins · 2026-01-30T09:51:52Z

how big is the data? can it be added to https://github.com/nf-core/test-datasets/ ?

16GB, so it cant go on test-datasets

eit-maxlcummins · 2026-01-30T09:52:59Z

Iteration time is super slow for testing etc because it has to download the 16gb file.

Additionally, the user agent mode which works is via wget - the default which gets blocked by zenodo parallelizes the download.

WGET takes 15-30 minutes to download this database, but doesnt get blocked by zenodo

mashehu · 2026-01-30T10:08:03Z

any way to make this database smaller to make testing easier?

eit-maxlcummins · 2026-01-30T10:53:10Z

any way to make this database smaller to make testing easier?

Well theres two modules - one is to download the database and one to run. In theory we could potentially make the checkm2 run module use a test one, but this doesnt help the checkm2/databasedownload module

mashehu · 2026-01-30T11:00:41Z

looks like other nf-core people are already on the case: nf-core/mag#915
we could maybe host it in our s3 bucket if you ask nicely on https://nfcore.slack.com/archives/C09H6NYHR9T 🙂

…m2 for setup in tests

eit-maxlcummins · 2026-02-02T15:22:50Z

Don't really understand how I can get these remaining tests to pass/why they are failing in the first place @mashehu

mashehu · 2026-02-02T15:28:36Z

the CI picks up all differences between master and your branch, so if other branches were merged into master they appear as tests in your PR until you update your branch again. Fixed it for you

eit-maxlcummins · 2026-02-02T16:33:15Z

That makes sense. Thanks! all passing now :)

modules/nf-core/checkm2/databasedownload/main.nf

modify version capture code Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

eit-maxlcummins · 2026-02-03T13:37:45Z

Tests are a bit iffy. They have passed now but I dont think they are particularly stable, potentially due to rate-limiting from zenodo - see https://blog.zenodo.org/2026/01/28/2026-01-28-improvements-and-support-expectations/

Now the database is also available at s3://nf-core-awsmegatests/mag/full_test_data/CheckM2_database/14897628/uniref100.KO.1.dmnd

Should we tweak to use the nf-core aws database?

(nf-core-dev) ubuntu@max-cummins:/mnt/blockvolume/nf-core/modules_contribution/versionathon_extra_modules/modules$ nf-core modules test checkm2/databasedownload --profile docker


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

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


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 CHECKM2_DATABASEDOWNLOAD                                                                                                                                                                                          │
│                                                                                                                                                                                                                                │
│   Test [411d2249] 'test_checkm2_databasedownload' PASSED (210.076s)                                                                                                                                                            │
│   Test [c3f0e706] 'test_checkm2_databasedownload - stub' PASSED (5.73s)                                                                                                                                                        │
│                                                                                                                                                                                                                                │
│ Test Process CHECKM2_PREDICT                                                                                                                                                                                                   │
│                                                                                                                                                                                                                                │
│   Test [915ac50a] 'test_checkm2_predict' PASSED (1503.935s)                                                                                                                                                                    │
│   Test [8ac6b352] 'test_checkm2_predict - stub' PASSED (23.587s)                                                                                                                                                               │
│                                                                                                                                                                                                                                │
│                                                                                                                                                                                                                                │
│ SUCCESS: Executed 4 tests in 1743.88s                                                                                                                                                                                          │
│                                                                                                                                                                                                                                │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
INFO     Generating nf-test snapshot again to check stability                                                                                                                                                                     
╭──────────────────────────────────────────────────────────────────────────────────────────────────────── 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 CHECKM2_DATABASEDOWNLOAD                                                                                                                                                                                          │
│                                                                                                                                                                                                                                │
│   Test [411d2249] 'test_checkm2_databasedownload' FAILED (144.162s)                                                                                                                                                            │
│                                                                                                                                                                                                                                │
│   Assertion failed:                                                                                                                                                                                                            │
│                                                                                                                                                                                                                                │
│   3 of 3 assertions failed                                                                                                                                                                                                     │
│                                                                                                                                                                                                                                │
│   Nextflow stdout:                                                                                                                                                                                                             │
│                                                                                                                                                                                                                                │
│   ERROR ~ Error executing process > 'CHECKM2_DATABASEDOWNLOAD'                                                                                                                                                                 │
│                                                                                                                                                                                                                                │
│   Caused by:                                                                                                                                                                                                                   │
│     Connection timed out -- Check script '/mnt/blockvolume/nf-core/modules_contribution/versionathon_extra_modules/modules/modules/nf-core/checkm2/databasedownload/main.nf' at line: 8                                        │
│                                                                                                                                                                                                                                │
│                                                                                                                                                                                                                                │
│   Source block:                                                                                                                                                                                                                │
│     def args = task.ext.args ?: ''                                                                                                                                                                                             │
│     if( !args.contains('--user-agent') ) {                                                                                                                                                                                     │
│         args = args ? "${args} --user-agent=\"Wget/1.21.4\"" : '--user-agent="Wget/1.21.4"'                                                                                                                                    │
│     }                                                                                                                                                                                                                          │
│     zenodo_id  = db_zenodo_id ?: 14897628                                                                                                                                                                                      │
│     api_data   = downloadZenodoApiEntry(zenodo_id)                                                                                                                                                                             │
│     db_version = api_data.metadata.version                                                                                                                                                                                     │
│     checksum   = api_data.files[0].checksum.replaceFirst(/^md5:/, "md5=")                                                                                                                                                      │
│     meta       = [id: 'checkm2_db', version: db_version]                                                                                                                                                                       │
│     """                                                                                                                                                                                                                        │
│     # Automatic download is broken when using singularity/apptainer (https://github.com/chklovski/CheckM2/issues/73)                                                                                                           │
│     # So it's necessary to download the database manually                                                                                                                                                                      │
│     aria2c \                                                                                                                                                                                                                   │
│         ${args} \                                                                                                                                                                                                              │
│         --checksum ${checksum} \                                                                                                                                                                                               │
│         https://zenodo.org/records/${zenodo_id}/files/checkm2_database.tar.gz                                                                                                                                                  │
│                                                                                                                                                                                                                                │
│     tar -xzf checkm2_database.tar.gz                                                                                                                                                                                           │
│     db_path=\$(find -name *.dmnd)                                                                                                                                                                                              │
│     mv \$db_path checkm2_db_v${db_version}.dmnd                                                                                                                                                                                │
│                                                                                                                                                                                                                                │
│     # cleanup                                                                                                                                                                                                                  │
│     rm -f checkm2_database.tar.gz                                                                                                                                                                                              │
│     """                                                                                                                                                                                                                        │
│                                                                                                                                                                                                                                │
│   Container:                                                                                                                                                                                                                   │
│     community.wave.seqera.io/library/aria2:1.37.0--3a9ec328469995dd                                                                                                                                                            │
│                                                                                                                                                                                                                                │
│   Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`                                                                                                        │
│                                                                                                                                                                                                                                │
│    -- Check '/mnt/blockvolume/nf-core/modules_contribution/versionathon_extra_modules/modules/.nf-test/tests/411d2249f2a241a7edea15bc2a6ac277/meta/nextflow.log' file for details                                              │
│   Nextflow stderr:                                                                                                                                                                                                             │
│                                                                                                                                                                                                                                │
│   Nextflow 25.10.3 is available - Please consider updating your version to it                                                                                                                                                  │
│                                                                                                                                                                                                                                │
│                                                                                                                                                                                                                                │
│   Test [c3f0e706] 'test_checkm2_databasedownload - stub' PASSED (10.624s)                                                                                                                                                      │
│     Obsolete snapshots can only be checked if all tests of a file are executed successful.                                                                                                                                     │
│                                                                                                                                                                                                                                │
│ Test Process CHECKM2_PREDICT                                                                                                                                                                                                   │
│                                                                                                                                                                                                                                │
│   Test [915ac50a] 'test_checkm2_predict' FAILED (144.352s)                                                                                                                                                                     │
│                                                                                                                                                                                                                                │
│   Assertion failed:                                                                                                                                                                                                            │
│                                                                                                                                                                                                                                │
│   2 of 2 assertions failed                                                                                                                                                                                                     │
│                                                                                                                                                                                                                                │
│   Nextflow stdout:                                                                                                                                                                                                             │
│                                                                                                                                                                                                                                │
│   ERROR ~ Error executing process > 'CHECKM2_DATABASEDOWNLOAD'                                                                                                                                                                 │
│                                                                                                                                                                                                                                │
│   Caused by:                                                                                                                                                                                                                   │
│     Connection timed out -- Check script '/mnt/blockvolume/nf-core/modules_contribution/versionathon_extra_modules/modules/modules/nf-core/checkm2/databasedownload/main.nf' at line: 8                                        │
│                                                                                                                                                                                                                                │
│                                                                                                                                                                                                                                │
│   Source block:                                                                                                                                                                                                                │
│     def args = task.ext.args ?: ''                                                                                                                                                                                             │
│     if( !args.contains('--user-agent') ) {                                                                                                                                                                                     │
│         args = args ? "${args} --user-agent=\"Wget/1.21.4\"" : '--user-agent="Wget/1.21.4"'                                                                                                                                    │
│     }                                                                                                                                                                                                                          │
│     zenodo_id  = db_zenodo_id ?: 14897628                                                                                                                                                                                      │
│     api_data   = downloadZenodoApiEntry(zenodo_id)                                                                                                                                                                             │
│     db_version = api_data.metadata.version                                                                                                                                                                                     │
│     checksum   = api_data.files[0].checksum.replaceFirst(/^md5:/, "md5=")                                                                                                                                                      │
│     meta       = [id: 'checkm2_db', version: db_version]                                                                                                                                                                       │
│     """                                                                                                                                                                                                                        │
│     # Automatic download is broken when using singularity/apptainer (https://github.com/chklovski/CheckM2/issues/73)                                                                                                           │
│     # So it's necessary to download the database manually                                                                                                                                                                      │
│     aria2c \                                                                                                                                                                                                                   │
│         ${args} \                                                                                                                                                                                                              │
│         --checksum ${checksum} \                                                                                                                                                                                               │
│         https://zenodo.org/records/${zenodo_id}/files/checkm2_database.tar.gz                                                                                                                                                  │
│                                                                                                                                                                                                                                │
│     tar -xzf checkm2_database.tar.gz                                                                                                                                                                                           │
│     db_path=\$(find -name *.dmnd)                                                                                                                                                                                              │
│     mv \$db_path checkm2_db_v${db_version}.dmnd                                                                                                                                                                                │
│                                                                                                                                                                                                                                │
│     # cleanup                                                                                                                                                                                                                  │
│     rm -f checkm2_database.tar.gz                                                                                                                                                                                              │
│     """                                                                                                                                                                                                                        │
│                                                                                                                                                                                                                                │
│   Container:                                                                                                                                                                                                                   │
│     community.wave.seqera.io/library/aria2:1.37.0--3a9ec328469995dd                                                                                                                                                            │
│                                                                                                                                                                                                                                │
│   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 '/mnt/blockvolume/nf-core/modules_contribution/versionathon_extra_modules/modules/.nf-test/tests/915ac50a5592a7301f151d3a62aa8fc1/meta/nextflow.log' file for details                                              │
│   Nextflow stderr:                                                                                                                                                                                                             │
│                                                                                                                                                                                                                                │
│   Nextflow 25.10.3 is available - Please consider updating your version to it                                                                                                                                                  │
│                                                                                                                                                                                                                                │
│                                                                                                                                                                                                                                │
│   Test [8ac6b352] 'test_checkm2_predict - stub' PASSED (23.141s)                                                                                                                                                               │
│     Obsolete snapshots can only be checked if all tests of a file are executed successful.                                                                                                                                     │
│                                                                                                                                                                                                                                │
│                                                                                                                                                                                                                                │
│ FAILURE: Executed 4 tests in 323.515s (2 failed)                                                                                                                                                                               │
│                                                                                                                                                                                                                                │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭──────────────────────────────────────────────────────────────────────────────────────────────────────── nf-test error ─────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ Assertion failed:                                                                                                                                                                                                              │
│                                                                                                                                                                                                                                │
│ assert process.success                                                                                                                                                                                                         │
│        |       |                                                                                                                                                                                                               │
│        |       false                                                                                                                                                                                                           │
│        CHECKM2_DATABASEDOWNLOAD                                                                                                                                                                                                │
│                                                                                                                                                                                                                                │
│ java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 0                                                                                                                                                          │
│ java.lang.RuntimeException: Different Snapshot:                                                                                                                                                                                │
│ --- /tmp/expected5695123690649215176jso +++ /tmp/found7040896856120000380json                                                                                                                                    │
│ n                                                                                                                                                                                                                 │
│ @@ -1,11 @@                             @@ +1,7 @@                                                                                                                                                               │
│    1 [                                    1 [                                                                                                                                                                                  │
│    2     {                                2     {                                                                                                                                                                              │
│    3         "versions_checkm2_database   3         "versions_checkm2_databased                                                                                                                                          │
│ download": [                            ownload": [                                                                                                                                                                │
│ !  4             [                      ! 4                                                                                                                                                           │
│ -  5                 "CHECKM2_DATABASED                                                                                                                                                                      │
│ OWNLOAD",                                                                                                                                                                                              │
│ -  6                 "aria2",                                                                                                                                                                                │
│ -  7                 "1.37.0"                                                                                                                                                                                │
│ -  8             ]                                                                                                                                                                                           │
│    9         ]                            5         ]                                                                                                                                                                          │
│   10     }                                6     }                                                                                                                                                                              │
│   11 ]                                    7 ]                                                                                                                                                                                  │
│                                                                                                                                                                                                                                │
│ Assertion failed:                                                                                                                                                                                                              │
│                                                                                                                                                                                                                                │
│ assert process.success                                                                                                                                                                                                         │
│        |       |                                                                                                                                                                                                               │
│        |       false                                                                                                                                                                                                           │
│        CHECKM2_PREDICT                                                                                                                                                                                                         │
│                                                                                                                                                                                                                                │
│ java.lang.RuntimeException: Different Snapshot:                                                                                                                                                                                │
│ --- /tmp/expected13609952045828551326js +++ /tmp/found17129292078906881043json                                                                                                                                   │
│ on                                                                                                                                                                                                                │
│ @@ -1,19 @@                             @@ +1,10 @@                                                                                                                                                              │
│    1 [                                     1 [                                                                                                                                                                                 │
│    2     [                                 2     [                                                                                                                                                                             │
│ !  3         [                          !  3                                                                                                                                                          │
│ -  4             {                                                                                                                                                                                           │
│ -  5                 "id": "test"                                                                                                                                                                            │
│ -  6             },                                                                                                                                                                                          │
│ -  7             "test_checkm2_report.t                                                                                                                                                                      │
│ sv:md5,1b6021262d336b21f526d8369f6ddd3f                                                                                                                                                                   │
│ "                                                                                                                                                                                                      │
│ -  8         ]                                                                                                                                                                                               │
│    9     ],                                4     ],                                                                                                                                                                            │
│   10     {                                 5     {                                                                                                                                                                             │
│   11         "versions_checkm2_predict"    6         "versions_checkm2_predict"                                                                                                                                          │
│ : [                                     : [                                                                                                                                                                        │
│ ! 12             [                      !  7                                                                                                                                                          │
│ - 13                 "CHECKM2_PREDICT",                                                                                                                                                                      │
│ - 14                 "checkm2",                                                                                                                                                                              │
│ - 15                 "1.1.0"                                                                                                                                                                                 │
│ - 16             ]                                                                                                                                                                                           │
│   17         ]                             8         ]                                                                                                                                                                         │
│   18     }                                 9     }                                                                                                                                                                             │
│   19 ]                                    10 ]                                                                                                                                                                                 │
│                                                                                                                                                                                                                                │
│                                                                                                                                                                                                                                │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
ERROR    nf-test failed due to differences in the snapshots                                                                                                                                                                       
ERROR    nf-test snapshot is not stable                                                                                                                                                                                           
CRITICAL Ran, but found errors:                                                                                                                                                                                                   
          - nf-test snapshot is not stable

eit-maxlcummins · 2026-02-03T13:37:58Z

Also, for future reference, Galah (which uses checkm2 in its test) sometimes produces a different snapshot - output is unstable.

Test Process GALAH

  Test [eb10124d] 'genomes - no qc_table' 
    > Nextflow 25.10.3 is available - Please consider updating your version to it
    > N E X T F L O W  ~  version 25.10.2
    > Launching `/home/runner/_work/modules/modules/.nf-test-eb10124dca308053ba7bc956ce5fc1bd.nf` [compassionate_saha] DSL2 - revision: 2666559059
    > WARN: There's no process matching config selector: CHECKM2_PREDICT
    > WARN: There's no process matching config selector: GAWK
    > [3f/b3a7a2] Submitted process > GALAH (test)
java.lang.RuntimeException: Different Snapshot:
--- /tmp/expected10537060661781350369js +++ /tmp/found7441176990397220540json  
on                                                                             
@@ -5,7 @@                              @@ +5,7 @@                             
   5                 {                     5                 {                 
   6                     "id": "test"      6                     "id": "test"  
   7                 },                    7                 },                
!  8                 "test.tsv:md5,d2f8 !  8                 "test.tsv:md5,e5fe
a621bfa5794467f4fdd759e2bce7"           3ac51e4f7cb0ee3050820905d826"          
   9             ]                         9             ]                     
  10         ],                           10         ],                        
  11         "1": [                       11         "1": [                    
@@ -38,7 @@                             @@ +38,7 @@                            
  38                 {                    38                 {                 
  39                     "id": "test"     39                     "id": "test"  
  40                 },                   40                 },                
! 41                 "test.tsv:md5,d2f8 ! 41                 "test.tsv:md5,e5fe
a621bfa5794467f4fdd759e2bce7"           3ac51e4f7cb0ee3050820905d826"          
  42             ]                        42             ]                     
  43         ],                           43         ],                        
  44         "versions": [                44         "versions": [             

    FAILED (11.896s)

@prototaxites to address Galah test data - thanks!

…m2 predict (nf-core#9744) Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: Julio DiazCaballero <jdiaz@eit.org>

eit-maxlcummins added 6 commits January 22, 2026 13:05

update to new versions capture for checkm2 databasedownload and check…

e7e07c3

…m2 predict

update tests and snapshots for topic versions

9539272

Merge branch 'master' into checkm2_versions

d711094

add trailing linebreak to test nextflow.config

210723e

add trailing linebreak to main.nf.test

7326d8d

Merge branch 'master' into checkm2_versions

444ba74

mashehu reviewed Jan 23, 2026

View reviewed changes

fix args function to prevent issues where users provide args but not …

f20d7c3

…--user-agent and jobs fail

eit-maxlcummins added 2 commits January 30, 2026 13:14

update checkm2 tests and snaps, and galah test and snaps - uses check…

d2c197a

…m2 for setup in tests

Merge branch 'master' into checkm2_versions

58cbb02

Merge branch 'master' into checkm2_versions

10f40aa

Merge branch 'master' into checkm2_versions

8ee3665

jdc-eit requested a review from mashehu February 3, 2026 00:52

mashehu reviewed Feb 3, 2026

View reviewed changes

modules/nf-core/checkm2/databasedownload/main.nf Outdated Show resolved Hide resolved

eit-maxlcummins and others added 6 commits February 3, 2026 09:05

Update modules/nf-core/checkm2/databasedownload/main.nf

2a683aa

modify version capture code Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Merge branch 'master' into checkm2_versions

5d01ce4

update meta.yml after change to version capture in main.nf

3450b41

Merge branch 'master' into checkm2_versions

7b1b52e

update checkm2/predict/meta.yml with lint --fix

3b51a12

update main.nf and meta.yml to pass linting

4fe8b4a

eit-maxlcummins added 3 commits February 3, 2026 10:31

Merge branch 'master' into checkm2_versions

cc655bf

Merge branch 'master' into checkm2_versions

8f5cb2a

Merge branch 'master' into checkm2_versions

0e2e63e

Merge branch 'master' into checkm2_versions

7edaca3

mashehu merged commit 81470b5 into nf-core:master Feb 3, 2026
38 checks passed

Conversation

eit-maxlcummins commented Jan 22, 2026

PR checklist

Uh oh!

mashehu Jan 23, 2026

Choose a reason for hiding this comment

Uh oh!

eit-maxlcummins Jan 30, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

eit-maxlcummins Jan 30, 2026

Choose a reason for hiding this comment

Uh oh!

eit-maxlcummins commented Jan 30, 2026

Uh oh!

mashehu commented Jan 30, 2026

Uh oh!

eit-maxlcummins commented Jan 30, 2026

Uh oh!

eit-maxlcummins commented Jan 30, 2026

Uh oh!

mashehu commented Jan 30, 2026

Uh oh!

eit-maxlcummins commented Jan 30, 2026

Uh oh!

mashehu commented Jan 30, 2026

Uh oh!

eit-maxlcummins commented Feb 2, 2026

Uh oh!

mashehu commented Feb 2, 2026

Uh oh!

eit-maxlcummins commented Feb 2, 2026

Uh oh!

Uh oh!

eit-maxlcummins commented Feb 3, 2026

Uh oh!

eit-maxlcummins commented Feb 3, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

eit-maxlcummins Jan 30, 2026 •

edited

Loading

eit-maxlcummins commented Feb 3, 2026 •

edited

Loading