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Hi all, thanks for the new nf-core/tools release! ...
# tools
g
Hi all, thanks for the new nf-core/tools release! I’m hitting a weird error when trying to run the pipeline linting locally 
nf-core p lint -d .
command, it doesn’t seem to find a pipeline in the directory even though I’m running it inside the airrflow pipeline repository (see log attached). It says 
ERROR    Pipeline repository not found in /tmp/tmp9ibmu6cd/nf-core-airrflow
. When following the link to that tmp directory, I also see that the version of the pipeline there does not correspond to the branch I’m trying to lint, super weird.
Untitled
m
can you try running it with 
nf-core --verbose p lint
?
g
Sure, here is the ouput
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m
what nextflow version do you have?
g
Copy code
nextflow -v
nextflow version 26.04.0.12031
m
can you try it wit 25.10 please? 26.04 changed some directory structure
👍 1
g
When running nf-core tools v3.5.2 the command finishes fine, there is a critical lint error but it still continues linting, in case this is useful
Untitled
It seems to run into the same issue
Untitled
The weird bit is that it says:
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prettier.................................................................Failed
         - hook id: prettier
         - exit code: 2

          ../../../../../tmp/tmpw0bhln3_/nf-core-airrflow/assets/adaptivecard.json: SyntaxError: Unexpected token (57:47)
            55 |                                 {
            56 |                                     "type": "FactSet",
          > 57 |                                     "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %>
               |                                               ^
            58 |                                     ]
            59 |                                 }
            60 |                             ]
         ../../../../../tmp/tmpw0bhln3_/nf-core-airrflow/README.md

          ../../../../../tmp/tmpw0bhln3_/nf-core-airrflow/assets/slackreport.json: SyntaxError: Unexpected token (15:18)
            13 |                     "short": false
            14 |                 }
          > 15 |                 <%
               |                  ^
            16 |                     if (!success) { %>
            17 |                     ,
            18 |                     {
         ../../../../../tmp/tmpw0bhln3_/nf-core-airrflow/.github/workflows/nf-test.yml
However there is no 
adaptivecard.json
or 
slackreport.json
in the assets directory of the pipeline version I’m testing
m
what is the directory you are currently in?
g
/home/gisela/Projects/Pipelines/nf-core-airrflow
m
i am confused by 
ERROR    Pipeline repository not found in /tmp/tmpv1pcaz_r/nf-core-airrflow
g
I know this is the weird bit
m
can you run the command without 
-d .
?
g
Same error
Untitled
I’ll try running it outside of the VS code terminal, one sec
m
what do you get when you run 
nextflow inspect
?
g
Nothing changed in the terminal outside VS code
Untitled
Untitled
m
do you know why you get 
Monitor the execution with Seqera Platform using this URL: <https://cloud.seqera.io/user/gisela-gabernet/watch/1mGYZTrqbhPQAu>
above the output?
this breaks the json parsing...
g
hmm no I don’t know why
Well in general I have Platform set up to follow my runs and it prints this message when I run a pipeline. I guess there’s no need to print it for the inspect command, but apparently Nextflow does.
m
yes, that is also my guess
can you try 
TOWER_ENABLED=false nextflow inspect .
g
What you suggested does not get rid of the message, however if I change my nextflow config to set enabled=false it does
👍🏻 1
m
then linting should work (the change in 4.0.0 is the we run that command to get the new container configs)
g
ah I see, I’ll try it out
👍🏻 1
I’m getting another error now, linting progressed further though:
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NotADirectoryError: [Errno 20] Not a directory: 'modules/local/enchantr/report_file_size.nf/meta.yml'
I do have some local modules that do not have a 
meta.yml
file, I guess I should update that
It’s weird cause for other modules it just listed them as the meta.yml file was not found, but for this one it threw an error.
Untitled
No worries, I’ve solved this. It works now!
Thank you so much @mashehu for the quick support 🙌
a
For the slack report/email thing this was the cause but you can see that it should no longer be an issue in newer versions
p
Above PR should fix this
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