Hi everyone, I've been struggling with this PR https://github.com/nf-core/modules/pull/9546/changes#diff-e0f9ddfba349bd1f4a77676c200d93bf7aa812c5a873c00dad8f71e1f625de24 for the

rseqc_innerdistance

module, I get this (only) error when linting

test_snap_versions: versions not found in snapshot file

but when I try to update the snapshot, I get this error (even though those assertions work fine for the other modules)

(nf_core_dev_env) rhassaine@rayan-nextflow-clean:~/modules/modules/nf-core/rseqc/innerdistance$ nf-core modules test rseqc/innerdistance --update


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

    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 0.9.2                                                                                                  │
│ <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                                                             │
│ Warning: every snapshot that fails during this test run is re-record.                                             │
│                                                                                                                   │
│ Test Process RSEQC_INNERDISTANCE                                                                                  │
│                                                                                                                   │
│   Test [76001645] 'sarscov2 - [[meta] - bam] - bed' PASSED (7.493s)                                               │
│   Test [d14387f8] 'sarscov2 - [[meta] - bam] - bed - stub' PASSED (7.04s)                                         │
│   Snapshots:                                                                                                      │
│     1 updated [sarscov2 - [[meta] - bam] - bed - stub]                                                            │
│                                                                                                                   │
│ Test Workflow BAM_RSEQC                                                                                           │
│                                                                                                                   │
│   Test [ac1caf66] 'sarscov2 paired-end [bam]' PASSED (10.309s)                                                    │
│   Test [65725b8e] 'sarscov2 paired-end [bam] no modules' FAILED (134.85s)                                         │
│                                                                                                                   │
│   Assertion failed:                                                                                               │
│                                                                                                                   │
│   10 of 10 assertions failed                                                                                      │
│                                                                                                                   │
│   Nextflow stdout:                                                                                                │
│                                                                                                                   │
│   ERROR ~ No such file or directory:                                                                              │
│ <https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_e> │
│ nd.sorted.bam.bai                                                                                                 │
│                                                                                                                   │
│    -- Check script '/home/rhassaine/modules/.<http://nf-test-65725b8e23fb5f978868b4e57190817a.nf|nf-test-65725b8e23fb5f978868b4e57190817a.nf>' at line: 35 or see      │
│ '/home/rhassaine/modules/.nf-test/tests/65725b8e23fb5f978868b4e57190817a/meta/nextflow.log' file for more details │
│   Nextflow stderr:                                                                                                │
│                                                                                                                   │
│                                                                                                                   │
│                                                                                                                   │
│   Test [de7683ba] 'sarscov2 paired-end [bam] - stub' PASSED (10.425s)                                             │
│   Test [9106a9dc] 'sarscov2 paired-end [bam] no modules - stub' PASSED (5.854s)                                   │
│     Obsolete snapshots can only be checked if all tests of a file are executed successful.                        │
│                                                                                                                   │
│                                                                                                                   │
│ Snapshot Summary:                                                                                                 │
│   1 updated                                                                                                       │
│                                                                                                                   │
│ FAILURE: Executed 6 tests in 176.025s (1 failed)                                                                  │
│                                                                                                                   │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭────────────────────────────────────────────────── nf-test error ──────────────────────────────────────────────────╮
│ Assertion failed:                                                                                                 │
│                                                                                                                   │
│ assert workflow.success                                                                                           │
│        |        |                                                                                                 │
│        workflow false                                                                                             │
│                                                                                                                   │
│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.                        │
│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.                        │
│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.                        │
│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.                        │
│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.                        │
│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.                        │
│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.                        │
│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.                        │
│ java.lang.RuntimeException: Workflow has no output channels. workflow.out can not be used.                        │
│                                                                                                                   │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
CRITICAL Ran, but found errors:
          - nf-test failed

Appreciative of any help 🙏

I think you should remove the versions entirely from the subworkflow if you have swapped all the modules. @Maxime Garcia, @Matthias De Smet

?

I already did that in the subworkflow, no ?

To be fully honest, I only launch the tests via nf-test directly, never via tools homer disappear