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I'm not sure how I triggered this, but after a reb...
# tools
p
I'm not sure how I triggered this, but after a rebase -i --autosquash, 
nf-core pipelines lint
suddenly stopped working. It seems to fail in the final step with a long trace and the following errors:
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GitCommandError: Cmd('git') failed due to: exit code(1)
  cmdline: git checkout 6d46786420b4d7bc88eba026eb389c0c5535d120
  stderr: 'error: The following untracked working tree files would be overwritten by checkout:
        modules/nf-core/bigslice/environment.yml
        modules/nf-core/bigslice/main.nf
        modules/nf-core/bigslice/meta.yml
        modules/nf-core/bigslice/tests/main.nf.test
        modules/nf-core/bigslice/tests/main.nf.test.snap
        modules/nf-core/bigslice/tests/nextflow.config
        modules/nf-core/faqcs/tests/faqcs_options.config
        modules/nf-core/faqcs/tests/faqcs_qc_only.config
        modules/nf-core/graphtyper/vcfconcatenate/tests/nextflow.config
        modules/nf-core/gstama/merge/tests/nextflow.config
        modules/nf-core/gstama/polyacleanup/tests/nextflow.config
        modules/nf-core/gt/ltrharvest/tests/nextflow.extended.config
        modules/nf-core/gt/ltrharvest/tests/nextflow.extended.custom.config
        modules/nf-core/happy/ftxpy/tests/feature.config
        modules/nf-core/homer/maketagdirectory/tests/bed.config
        modules/nf-core/homer/maketagdirectory/tests/sam.config
        modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt
        modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt
Several of those modules are ones that are unused in the pipeline, so my guess these untracked files are actually in the TEMPLATE branch, not my current one? I can provide a more detailed trace and description of what the rebase did, if necessary. Any ideas? I'm a bit stumped.
m
Some of these files are defintively not coming from the template
I usually don't ship the 
*/nf-core/**/tests
with my pipelines as I believe the modules are already properly tested upstream. That would solve half your issues already.
For the rest I would try to force reinstall of the modules, and trying to make sure all files are properly in staging and or commited
But I am fairly certain, @mashehu has a smarter solution
m
are you sure you have a clean working tree?
party this 1
m
I tend to hack my way through the TEMPLATE sync
m
and if you have a PR with it handy, I could give it a closer look
p
My own git dir is clean (stashed). The only thing that changed between the linting working and not-working is a single commit --fixup + rebase. Checking out a previous commit prior to the rebase point also produces errors. There's no PR cause this is a non-nf-core pipeline 😞 (need to head to a meeting but can provide more info later, thanks for the suggestions so far though!)
The plot thickens. A fresh clone, checked out on a commit from yesterday, also results in the same error.
Are there any machine-wide states saved by the nf-core tools package in a config or tmp dir somewhere?
m
yes, the module cache. can you remove 
~/.config/nfcore/nf-core/modules
p
Huzzah! That was it. What a relief!
Thank you so much. I was sweating there for a second.
m
sorry, should have guessed that earlier
p
Not at all! I'm just happy to have such a convenient help desk available nearly 24/7 🙂
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