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Hey hey, I made a little oopsie using nf-core tool...
# tools
t
Hey hey, I made a little oopsie using nf-core tools and wonder if there is a trivial way to fix it: 1. I wanted to update the bcl_demultiplex swf, so I did 
nf-core swf update
2. Then there was this intermediate question
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WARNING  All modules and subworkflows linked to the updated subworkflow will be automatically updated.                                                                   
         It is advised to keep all your modules and subworkflows up to date.                                                                                             
         It is not guaranteed that a subworkflow will continue working as expected if all modules/subworkflows used in it are not up to date.                            
                                                                                                                                                                         
? Would you like to continue updating all modules and subworkflows? No
INFO     Updates complete ✨
3. I chose "No" because I thought this would refer to all modules and swf in my pipeline. (which I really don't want to do!) 4. Now, the new bcl_demultiplex swf is missing the multiqcsav module. I assume the previous decision was about updating all modules/subworkflows linked to bcl_demultiplex? This message in (2) was confusing/misleading to me. 5. Then I tried 
nf-core swf update
again, as well as 
nf-core m update
and 
nf-core m install
but they all end up in an error now
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$ nf-core m install


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\ 
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.5.2 - <https://nf-co.re>


ERROR    'multiqcsav'
6. Now it seems that I broke nf-core tools on my side, likely because the modules.json doesn't match my present modules (multiqcsav missing). I could patch this by hand copying all the files from the multiqcsav module plus editing the modules.json. But is there a ways to fix this via nf-core tools?
m
can you try to install it with 
--force
? and run the command with 
nf-core --verbose swf install
t
Copy code
$ nf-core m install --force multiqcsav


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\ 
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.5.2 - <https://nf-co.re>


ERROR    'multiqcsav'
m
try it with 
--verbose
and can post your 
modules.jon
here
can you try to remove your modules cache at 
/pathToMyHome/.config/nfcore
and retry?
🆗 1
t
$ nf-core --verbose swf install
still resulting in 
ERROR    'multiqcsav'
m
from what line is the error coming from (you cut off that log message in the last log I think)
t
commands_subworkflows.py:204
Pardon. Should I paste the full stack again? (this needs a minute to get rid of local paths)
m
nope, that’s fine
👍 1
what happens if you try 
nf-core m install multiqcsav
t
Copy code
$ nf-core m install multiqcsav


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\ 
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.5.2 - <https://nf-co.re>


ERROR    'multiqcsav'
m
with the verbose log again please 🙂
nf-core m info multiqcsav
works for you?
t
no 😕
Copy code
$ nf-core m info multiqcsav


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\ 
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.5.2 - <https://nf-co.re>


ERROR    'multiqcsav'
m
can you try to remove 
<home>/.config/nfcore
and 
/<home>/.config/nf-core
(if they exist)
Can you run git status inside the modules cache?
t
Copy code
~/.config/nfcore/nf-core/modules$ git status
Refresh index: 100% (10625/10625), done.
On branch master
Your branch is up to date with 'origin/master'.


It took 3.91 seconds to enumerate untracked files.
See 'git help status' for information on how to improve this.

nothing to commit, working tree clean
@mashehu I massively appreciate your support! I have done the fixing by hand now 🥲
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