Does the latest nextflow (26.04.0) not work with n...
# nf-test
m
Does the latest nextflow (26.04.0) not work with nf-test?
confused dog 1
m
it works with 0.9.5
m
The error I'm getting
Copy code
nf-core modules test krakenuniq/build --profile docker


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

    nf-core/tools version 4.0.2 - <https://nf-co.re>


INFO     Generating nf-test snapshot
Displaying nf-test output
╭───────────────────────────────────────────────────────────────────────────────────────────────── nf-test output ──────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                                                                   │
│ 🚀 nf-test 0.9.2                                                                                                                                                                                                  │
│ <https://www.nf-test.com>                                                                                                                                                                                           │
...

│
│ Test Process KRAKENUNIQ_BUILD                                                                                                                                                                                     │
│                                                                                                                                                                                                                   │
│   Test [9da2fe17] 'sarscov2 - fasta' FAILED (3.583s)                                                                                                                                                              │
│                                                                                                                                                                                                                   │
│   java.lang.RuntimeException: Process has no output channels. process.out can not be used.                                                                                                                        │
│   Nextflow stdout:                                                                                                                                                                                                │
│                                                                                                                                                                                                                   │
│                                                                                                                                                                                                                   │
│   Error .<http://nf-test-9da2fe17321b589c5f1439ed7c2c8254.nf:35:29|nf-test-9da2fe17321b589c5f1439ed7c2c8254.nf:35:29>: Unexpected input: '*'                                                                                                                                 │
│   │  35 |         KRAKENUNIQ_DOWNLOAD(*input)                                                                                                                                                                     │
│   ╰     |                             ^                                                                                                                                                                           │
│                                                                                                                                                                                                                   │
│                                                                                                                                                                                                                   │
│   ERROR ~ Script compilation failed                                                                                                                                                                               │
│                                                                                                                                                                                                                   │
│    -- Check '/Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.nf-test/tests/9da2fe17321b589c5f1439ed7c2c8254/meta/nextflow.log' file for details                                                        │
│   Nextflow stderr:                                                                                                                                                                                                │
│                                                                                                                                                                                                                   │
│                                                                                                                                                                                                                   │
│                                                                                                                                                                                                                   │
│   Test [4bc007d8] 'sarscov2 - fasta - nocleanup' FAILED (2.42s)                                                                                                                                                   │
│                                                                                                                                                                                                                   │
│   java.lang.RuntimeException: Process has no output channels. process.out can not be used.                                                                                                                        │
│   Nextflow stdout:                                                                                                                                                                                                │
│                                                                                                                                                                                                                   │
│                                                                                                                                                                                                                   │
│   Error .<http://nf-test-4bc007d857edf0060d601b4f39a59345.nf:35:29|nf-test-4bc007d857edf0060d601b4f39a59345.nf:35:29>: Unexpected input: '*'                                                                                                                                 │
│   │  35 |         KRAKENUNIQ_DOWNLOAD(*input)                                                                                                                                                                     │
│   ╰     |                             ^                                                                                                                                                                           │
│                                                                                                                                                                                                                   │
│                                                                                                                                                                                                                   │
│   ERROR ~ Script compilation failed                                                                                                                                                                               │
│                                                                                                                                                                                                                   │
│    -- Check '/Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.nf-test/tests/4bc007d857edf0060d601b4f39a59345/meta/nextflow.log' file for details                                                        │
│   Nextflow stderr:                                                                                                                                                                                                │
│                                                                                                                                                                                                                   │
│                                                                                                                                                                                                                   │
│                                                                                                                                                                                                                   │

...

Displaying nf-test error
CRITICAL Ran, but found errors:
          - nf-test failed
          - Assertion failed.
Looks like the spread
input
is causing issues
m
yes, you need to update your nf-test
m
huh. I thought I updated nf-test
will do again
Oh, there's no
nf-test
in the pixi env. It's somehow coming from the
nf-core
recipe