I hope this is perhaps a quick answer I am trying to do nf c nf-core #linting

I hope this is perhaps a quick answer. I am tryin...

Andy Pohl

01/29/2025, 2:21 PM

I hope this is perhaps a quick answer. I am trying to do "nf-core pipelines lint" and as of like a month ago it would scan through a lot of checks and give a full report of warnings and errors. Now it abruptly stops shortly after starting to run with this message:

Copy code

ERROR    repository url must be like <https://github.com/><OWNER>/<REPO>

Which setting is it complaining about? Thanks.

Júlia Mir

01/29/2025, 2:25 PM

can you run the command with the

--verbose

flag to get more information about the error? Like

nf-core --verbose pipelines lint

Andy Pohl

01/29/2025, 3:15 PM

Copy code

DEBUG    Popen(['git', 'cat-file', '--batch-check'], cwd=/Users/apohl/pipeline, stdin=<valid         cmd.py:1253
         stream>, shell=False, universal_newlines=False)                                                                                                  
DEBUG    Got '.' as path                                                                                                                      utils.py:280
DEBUG    Found a config cache, loading: /Users/apohl/.nextflow/nf-core/wf-config-cache-66786925160e2708c488abdbb.json                         utils.py:314
DEBUG    Using config file: .nf-core.yml                                                                                                     utils.py:1385
DEBUG    Got '.' as path                                                                                                                      utils.py:280
DEBUG    Found a config cache, loading: /Users/apohl/.nextflow/nf-core/wf-config-cache-66786925160e2708c488abdbb.json                         utils.py:314
INFO     Testing pipeline: .                                                                                                               __init__.py:198
DEBUG    Running lint test: files_exist                                                                                                    __init__.py:262
DEBUG    Running lint test: nextflow_config                                                                                                __init__.py:262
DEBUG    Got '.' as path                                                                                                                      utils.py:280
DEBUG    Found a config cache, loading: /Users/apohl/.nextflow/nf-core/wf-config-cache-66786925160e2708c488abdbb.json                         utils.py:314
DEBUG    Ignoring parameters from config: ['genomes']                                                                                        schema.py:107
DEBUG    Ignoring parameters: ['help', 'help_full', 'show_hidden', 'trace_report_suffix', 'genomes']                                         schema.py:110
DEBUG    JSON file loaded: nextflow_schema.json                                                                                              schema.py:192
DEBUG    Running lint test: files_unchanged                                                                                                __init__.py:262
DEBUG    Could not find a config file in the directory '/var/folders/s9/d5x3nx3x2s7b74_zc_h1fvhr0000gp/T/tmpbfnfa055/pipeline'  utils.py:1328
DEBUG    Could not find git hash for pipeline: /var/folders/s9/d5x3nx3x2s7b74_zc_h1fvhr0000gp/T/tmpbfnfa055/pipeline.            utils.py:179
         /var/folders/s9/d5x3nx3x2s7b74_zc_h1fvhr0000gp/T/tmpbfnfa055/pipeline                                                               
DEBUG    Got '/var/folders/s9/d5x3nx3x2s7b74_zc_h1fvhr0000gp/T/tmpbfnfa055/pipeline' as path                                     utils.py:280
DEBUG    Found a config cache, loading: /Users/apohl/.nextflow/nf-core/wf-config-cache-d9159a67db16a50f3d032e822.json                         utils.py:314
DEBUG    No conda `environment.yml` file found.                                                                                               utils.py:200
ERROR    repository url must be like <https://github.com/><OWNER>/<REPO>

Andy Pohl

01/29/2025, 3:16 PM

Thanks that gave a lot more info!

Júlia Mir

01/29/2025, 3:34 PM

What is the name of your pipeline? Did you create it using the nf-core template with

nf-core pipelines create

Júlia Mir

01/29/2025, 3:37 PM

you could check in any github URL is malformed, on your

nextflow.config

file under

manifest.homepage

or the

modules.json

file maybe?

Andy Pohl

01/29/2025, 3:51 PM

Thanks it's fixed! I had a setting in modules.json that wasn't the same as in nextflow.config.

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