Hello, I am trying to add a new module but I'm having some linting issues. The error message is:

Module meta.yml does not match <http://main.nf|main.nf>. Outputs should contain: {'tsv': [['meta', 'FusionInspector.fusions.tsv']], 'out_gtf': [['meta',  'fi_workdir/.gtf']], 'log': [['meta', '*FusionInspector.log']], 'html': [['meta', '*html']], 'abridged_tsv': [['meta', '*abridged.tsv']], 'igv_inputs': [['meta', 'IGV_inputs']], 'fi_workdir': [['meta', 'fi_workdir']], 'chckpts_dir': [['meta', 'chckpts_dir']], 'versions': ['versions.yml']} Run nf-core modules lint --fix to update the meta.yml file.

However, when I try to solve it using

--fix

I get "CRITICAL 0" (https://github.com/nf-core/modules/pull/8051). Can anyone help me with this?

We just updated the structure and the underlying tools today, so could be that you run into something unforseen. Which nf-core tools version are you using to fix the linting and could you add a --verbose as the second argument after nf-core (has to be on that position unfortunately) so we see a bit more of the error source?

Sure! This is the output:

nf-core/tools version 3.3.2.dev0 - <https://nf-co.re>


DEBUG    Popen(['git', 'version'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)                                                                  cmd.py:1253
DEBUG    Popen(['git', 'fetch', '-v', '--progress', '--', 'origin'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=True)                                 cmd.py:1253
DEBUG    Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)                                                       cmd.py:1253
DEBUG    Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)                                                   cmd.py:1253
DEBUG    Got '/home/gitpod/.config/nfcore/nf-core/modules' as path                                                                                                                                     utils.py:281
DEBUG    Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json                                                                                  utils.py:315
DEBUG    Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml                                                                                                                  utils.py:1407
DEBUG    Got '.' as path                                                                                                                                                                               utils.py:281
DEBUG    Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json                                                                                  utils.py:315
DEBUG    Using config file: .nf-core.yml                                                                                                                                                              utils.py:1407
DEBUG    Got 'tests/config' as path                                                                                                                                                                    utils.py:281
DEBUG    Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-878fa13381bd0f7224fb3046a.json                                                                                  utils.py:315
DEBUG    Registry set to <http://quay.io|quay.io>                                                                                                                                                                    __init__.py:163
INFO     Linting modules repo: '.'                                                                                                                                                                  __init__.py:154
INFO     Linting module: 'fusioninspector'                                                                                                                                                          __init__.py:158
DEBUG    Found 2 inputs in modules/nf-core/fusioninspector/main.nf                                                                                                                          nfcore_component.py:228
DEBUG    Found 9 outputs in modules/nf-core/fusioninspector/main.nf                                                                                                                         nfcore_component.py:280
DEBUG    Correct outputs: '{'tsv': [['meta', '*FusionInspector.fusions.tsv']], 'out_gtf': [['meta', 'fi_workdir/*.gtf']], 'log': [['meta', '*FusionInspector.log']], 'html': [['meta', '*html']],   __init__.py:352
         'abridged_tsv': [['meta', '*abridged.tsv']], 'igv_inputs': [['meta', 'IGV_inputs']], 'fi_workdir': [['meta', 'fi_workdir']], 'chckpts_dir': [['meta', 'chckpts_dir']], 'versions':                        
         ['versions.yml']}' differ from current outputs: '{'tsv': [['meta', 'FusionInspector.fusions.tsv']], 'out_gtf': [['meta', 'fi_workdir/.gtf']], 'log': [['meta', '*FusionInspector.log']],                  
         'html': [['meta', '*html']], 'abridged_tsv': [['meta', '*abridged.tsv']], 'igv_inputs': [['meta', 'IGV_inputs']], 'fi_workdir': [['meta', 'fi_workdir']], 'chckpts_dir': [['meta',                        
         'chckpts_dir']], 'versions': ['versions.yml']}' in 'modules/nf-core/fusioninspector/meta.yml'                                                                                                             
CRITICAL 0

Hi @Delfina Terradas, I pushed a commit to your PR updating the meta.yml of the module

Thank you!

should be fixed in the newly released 3.3.2. thanks for reporting the bug!