I've installed the dev version of tools to try and...
# toolsi
Igor Trujnara
07/09/2026, 11:18 AMI've installed the dev version of tools to try and fix a linting error in CI and apparently it crashes on any command because it can't parse the version?
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│ /opt/conda/lib/python3.13/re/__init__.py:208 in sub │
│ │
│ 205 │ │ │ DeprecationWarning, stacklevel=2 │
│ 206 │ │ ) │
│ 207 │ │
│ ❱ 208 │ return _compile(pattern, flags).sub(repl, string, count) │
│ 209 sub.__text_signature__ = '(pattern, repl, string, count=0, flags=0)' │
│ 210 │
│ 211 def subn(pattern, repl, string, *args, count=_zero_sentinel, flags=_zero_sentinel): │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
TypeError: expected string or bytes-like object, got 'NoneType'm
mashehu
07/09/2026, 11:35 AMcan you try to run it with
nf-core --verbosei
Igor Trujnara
07/09/2026, 11:57 AMThis is the full output of
nf-core --verbose Copy code
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version None - <https://nf-co.re>
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /opt/conda/bin/nf-core:6 in <module> │
│ │
│ 3 from nf_core.__main__ import run_nf_core │
│ 4 if __name__ == '__main__': │
│ 5 │ sys.argv[0] = sys.argv[0].removesuffix('.exe') │
│ ❱ 6 │ sys.exit(run_nf_core()) │
│ 7 │
│ │
│ /opt/conda/lib/python3.13/site-packages/nf_core/__main__.py:124 in run_nf_core │
│ │
│ 121 │ │ │ highlight=False, │
│ 122 │ │ ) │
│ 123 │ │ try: │
│ ❱ 124 │ │ │ is_outdated, _, remote_vers = check_if_outdated() │
│ 125 │ │ │ if is_outdated: │
│ 126 │ │ │ │ stderr.print( │
│ 127 │ │ │ │ │ f"[bold bright_yellow] There is a new version of nf-core/tools av │
│ │
│ /opt/conda/lib/python3.13/site-packages/nf_core/utils.py:172 in check_if_outdated │
│ │
│ 169 │ # Set and clean up the current version string │
│ 170 │ if current_version is None: │
│ 171 │ │ current_version = nf_core.__version__ │
│ ❱ 172 │ current_version = re.sub(r"[^0-9\.]", "", current_version) │
│ 173 │ # Build the URL to check against │
│ 174 │ source_url = os.environ.get("NFCORE_VERSION_URL", source_url) │
│ 175 │ source_url = f"{source_url}?v={current_version}" │
│ │
│ /opt/conda/lib/python3.13/re/__init__.py:208 in sub │
│ │
│ 205 │ │ │ DeprecationWarning, stacklevel=2 │
│ 206 │ │ ) │
│ 207 │ │
│ ❱ 208 │ return _compile(pattern, flags).sub(repl, string, count) │
│ 209 sub.__text_signature__ = '(pattern, repl, string, count=0, flags=0)' │
│ 210 │
│ 211 def subn(pattern, repl, string, *args, count=_zero_sentinel, flags=_zero_sentinel): │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
TypeError: expected string or bytes-like object, got 'NoneType'm
mashehu
07/09/2026, 11:59 AMwhat was the exact command you ran?
i
Igor Trujnara
07/09/2026, 12:00 PMnf-core --verbosenf-core p lintm
mashehu
07/09/2026, 12:04 PMcan you run
pip install --upgrade --force-reinstall git+<https://github.com/nf-core/tools.git@dev>i
Igor Trujnara
07/09/2026, 1:34 PMNew error, this time from pip
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× Cannot uninstall nf-core None
╰─> The package's contents are unknown: no RECORD file was found for nf-core.Igor Trujnara
07/09/2026, 2:25 PMI fixed it and reinstalled, now I'm getting a new error:
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│ /root/nf-core/lib/python3.13/site-packages/nf_core/pipelines/lint/files_exist.py:201 in │
│ files_exist │
│ │
│ 198 │ │ Path("lib", "Utils.groovy"), │
│ 199 │ │ Path("lib", "Workflow.groovy"), │
│ 200 │ │ Path("lib", "WorkflowMain.groovy"), │
│ ❱ 201 │ │ Path("lib", f"Workflow{short_name[0].upper()}{short_name[1:]}.groovy"), │
│ 202 │ │ Path("parameters.settings.json"), │
│ 203 │ │ Path("pipeline_template.yml"), # saving information in .nf-core.yml │
│ 204 │ │ Path("Singularity"), │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
IndexError: string index out of rangeIgor Trujnara
07/09/2026, 2:26 PMI can send the full stacktrace if needed
m
mashehu
07/09/2026, 2:28 PMhow does your manifest in nextflow.config look like?
i
Igor Trujnara
07/09/2026, 2:29 PM Copy code
manifest {
name = 'nf-core/reportho'
contributors = [
[
name: 'Igor Trujnara',
affiliation: 'Centre for Genomic Regulation',
email: '<mailto:igor.trujnara@crg.eu|igor.trujnara@crg.eu>',
github: 'itrujnara',
contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: '0000-0002-8735-5976'
],
[
name: 'Luisa Santus',
affiliation: 'Centre for Genomic Regulation',
email: '<mailto:luisa.santus@crg.eu|luisa.santus@crg.eu>',
contribution: ['contributor'],
orcid: '0000-0002-5992-0771'
],
[
name: 'Jose Espinosa-Carrasco',
affiliation: 'Centre for Genomic Regulation',
email: '<mailto:jose.espinosa@crg.eu|jose.espinosa@crg.eu>',
contribution: ['contributor'],
orcid: '0000-0002-1541-042X'
],
[
name: 'Alessio Vignoli',
affiliation: 'Centre for Genomic Regulation',
email: '<mailto:alessio.vignoli@crg.eu|alessio.vignoli@crg.eu>',
contribution: ['contributor'],
orcid: '0000-0001-7131-2915'
]
]
homePage = '<https://github.com/nf-core/reportho>'
description = """A pipeline for ortholog fetching and analysis"""
mainScript = '<http://main.nf|main.nf>'
defaultBranch = 'main'
nextflowVersion = '!>=25.10.4'
version = '1.2.0dev'
doi = '10.5281/zenodo.11574565'
}m
mashehu
07/09/2026, 2:43 PMdo you have a PR that i can check?
i
Igor Trujnara
07/09/2026, 2:48 PMBest I can do: github.com/nf-core/reportho/pull/131
Igor Trujnara
07/09/2026, 2:58 PMA well-scoped commit saved the day, that does not solve the crazy tools in the codespace. I'll return to it when it bites again.
m
mashehu
07/09/2026, 2:59 PMyou have an outdated cache (we switched how we parse configs in dev): remove
~/.nextflow/nf-core/i
Igor Trujnara
07/09/2026, 3:05 PMThanks, it worked. It's always a cache. Now I can go back to going insane about strict syntax.
m
mashehu
07/09/2026, 3:06 PMchristmas-special-party-gif-by-all-creatures-great-and-small.gif
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