Is the `.nf-core.yml` documented somewhere? I'm gu...
# toolsm
Mahesh Binzer-Panchal
05/04/2026, 2:19 PMIs the
.nf-core.ymlprekm
mashehu
05/04/2026, 2:23 PMif you add it to .gitignore it will be ignored
mashehu
05/04/2026, 2:23 PMor
.prettierignoremashehu
05/04/2026, 2:24 PMcan you give me the exact error?
m
Mahesh Binzer-Panchal
05/04/2026, 2:26 PM Copy code
% pixi run nf-core-sync
✨ Pixi task (nf-core-sync): nf-core pipelines sync
<frozen importlib._bootstrap>:491: RuntimeWarning: The global interpreter lock (GIL) has been enabled to load module '_brotli', which has not declared that it can run safely without the GIL. To override this behavior and keep the GIL disabled (at your own risk), run with PYTHON_GIL=0 or -Xgil=0.
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 4.0.2 - <https://nf-co.re>
/Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/lib/python3.14t/site-packages/click/core.py:1252: UserWarning: The parameter -b is used more than once. Remove its duplicate as parameters should be unique.
parser = self.make_parser(ctx)
/Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/lib/python3.14t/site-packages/click/core.py:1245: UserWarning: The parameter -b is used more than once. Remove its duplicate as parameters should be unique.
self.parse_args(ctx, args)
WARNING Could not find GitHub authentication token. Some API requests may fail.
INFO Pipeline directory: /Users/mahpa906/Documents/Projects/nf-core-aMeta
INFO Original pipeline repository branch is 'master'
INFO Deleting tracked files in 'TEMPLATE' branch
INFO Making a new template pipeline using pipeline variables
INFO Using found ORCID for Mahesh Binzer-Panchal. Please double-check: <https://orcid.org/0000-0003-1675-0677>
INFO Saving metadata file to '/Users/mahpa906/Documents/Projects/nf-core-aMeta'
INFO Generated container configs for the pipeline successfully.
ERROR Failed to rebuild pipeline from template with error:
[Errno 7] Argument list too long: '/Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/bin/prek'Mahesh Binzer-Panchal
05/04/2026, 2:27 PMIt comes from the template branch which gets reset and doesn't have
.pixim
mashehu
05/04/2026, 2:29 PMnf-core --verbose pipelines syncm
Mahesh Binzer-Panchal
05/04/2026, 2:31 PM Copy code
DEBUG Running command: nextflow -v utils.py:480
DEBUG Detected Nextflow version 26.04.0 utils.py:365
DEBUG Generating container config file with nextflow inspect. containers_utils.py:105
DEBUG Running command: nextflow inspect -format json /Users/mahpa906/Documents/Projects/nf-core-aMeta utils.py:480
DEBUG Found 2 modules: FASTQC, MULTIQC containers_utils.py:122
DEBUG Found include: FASTQC -> modules/nf-core/fastqc containers_utils.py:86
DEBUG Found include: MULTIQC -> modules/nf-core/multiqc containers_utils.py:86
DEBUG Parsed 2 module paths from include statements containers_utils.py:126
DEBUG Using parsed path for FASTQC: modules/nf-core/fastqc containers_utils.py:140
DEBUG Loaded meta.yml for FASTQC from /Users/mahpa906/Documents/Projects/nf-core-aMeta/modules/nf-core/fastqc/meta.yml containers_utils.py:152
DEBUG Found docker_amd64 container for FASTQC containers_utils.py:161
DEBUG Found docker_arm64 container for FASTQC containers_utils.py:161
DEBUG Found singularity_oras_amd64 container for FASTQC containers_utils.py:161
DEBUG Found singularity_oras_arm64 container for FASTQC containers_utils.py:161
DEBUG Found singularity_https_amd64 container for FASTQC containers_utils.py:161
DEBUG Found singularity_https_arm64 container for FASTQC containers_utils.py:161
DEBUG Found conda_lock_files_amd64 container for FASTQC containers_utils.py:161
DEBUG Found conda_lock_files_arm64 container for FASTQC containers_utils.py:161
DEBUG Using parsed path for MULTIQC: modules/nf-core/multiqc containers_utils.py:140
DEBUG Loaded meta.yml for MULTIQC from /Users/mahpa906/Documents/Projects/nf-core-aMeta/modules/nf-core/multiqc/meta.yml containers_utils.py:152
DEBUG Found docker_amd64 container for MULTIQC containers_utils.py:161
DEBUG Found docker_arm64 container for MULTIQC containers_utils.py:161
DEBUG Found singularity_oras_amd64 container for MULTIQC containers_utils.py:161
DEBUG Found singularity_oras_arm64 container for MULTIQC containers_utils.py:161
DEBUG Found singularity_https_amd64 container for MULTIQC containers_utils.py:161
DEBUG Found singularity_https_arm64 container for MULTIQC containers_utils.py:161
DEBUG Found conda_lock_files_amd64 container for MULTIQC containers_utils.py:161
DEBUG Found conda_lock_files_arm64 container for MULTIQC containers_utils.py:161
INFO Generated container configs for the pipeline successfully. containers_utils.py:171
DEBUG sys.platform='darwin', git_executable='git' util.py:494
DEBUG Popen(['git', 'reset', '--hard'], cwd=/Users/mahpa906/Documents/Projects/nf-core-aMeta, stdin=None, shell=False, universal_newlines=False) cmd.py:1286
ERROR Failed to rebuild pipeline from template with error: commands_pipelines.py:363
[Errno 7] Argument list too long: '/Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/bin/prek'f
Felix Lenner
05/05/2026, 5:15 AMGetting the same error trying to sync for https://github.com/genomic-medicine-sweden/nallo, but I'm not using Pixi.
m
mashehu
05/05/2026, 5:31 AMLooked into the logic again and looks like we don't skip ignored files on that level. Will add that in a patch release
mashehu
05/05/2026, 5:32 AMIn the mean time you can try to remove directories with many files, e.g. work/ or .nf-test/
m
Mahesh Binzer-Panchal
05/05/2026, 6:57 AMFull clean doesn't help ( there wasn't much anyway ).
f
Felix Lenner
05/05/2026, 6:58 AMWorked for me at least, thanks @mashehu
b
Beatriz Sá Vinhas
05/05/2026, 12:00 PMI got the same error, using
condaz
Zachary Norgaard
06/08/2026, 3:15 PM@Mahesh Binzer-Panchal the problem if you keep using pixi is it rebuilds the environment when you call it, so recreates all the files when you try to run sync using it.
I worked around that by cleaning up all the files then switching to a conda env temporarily. We could also fix this permanently by batching the calls in nf-core/tools.
https://github.com/nf-core/tools/pull/4123
m
Mahesh Binzer-Panchal
06/08/2026, 6:58 PMThanks. I think I worked around it at the time by using
pixi global2 Views