nf-core / nf-core/tools

Updating the modules.json file to new format results in branch lookup error

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#1,824 3 comments 0 reactions 1 assignee View on GitHub

@mirpedrol is already working on this.

Since Sep 20, 2022.

bug
Dominant language
Python
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Avg merge
2d 3h
Merged PRs (30d)
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Description

Description of the bug

On this branch https://github.com/mahesh-panchal/Earth-Biogenome-Project-pilot/tree/update_prepare_input
when I use the command nf-core modules update -a in Gitpod: https://gitpod.io/#https://github.com/mahesh-panchal/Earth-Biogenome-Project-pilot/tree/update_prepare_input, fails to update the modules.json file to the new format.
It prompts me for the following:

INFO     The 'modules.json' file is not up to date. Recreating the 'module.json' file.                                                                                      modules_json.py:439
INFO     Was unable to find matching module files in the master branch.                                                                                                     modules_json.py:231
? Was the modules installed from a different branch in the remote? (Use arrow keys)
 » No
   bump-kbtools
   Test_unsetJAVA
   humann
   elixir
   greater-than-256
   merge
   fastqvalidator
   jwarnn-patch-1
   trimmomatic
   head

and then cannot find the branch "No".

Command used and terminal output
$ nf-core modules update -a

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

    nf-core/tools version 2.5.1 - https://nf-co.re


WARNING  modules.json entry {'blast/blastn': {'git_sha': 'e745e167c1020928ef20ea1397b6b4d230681b4d'}, 'busco': {'git_sha': '9fa6b6c1fc930830c1d819a9273b4ec12ffacb0a'},     modules_json.py:373
         'diamond/blastx': {'git_sha': 'bd3bfe0817246082525ab93707976676b1fe208b'}, 'fastk/fastk': {'git_sha': '4e308c131e29bc2cca3d46ba8f7e59e9d3785198'}, 'fastk/histex':                    
         {'git_sha': 'fd5aea0b76c1e5b908191f212382a55a57cee316'}, 'genescopefk': {'git_sha': 'e91e99db30c143ed913313301b53b5454df8720d'}, 'genomescope2': {'git_sha':                          
         'd54cf467f47461e8304e6fc4a4a1192869bfd792'}, 'mash/screen': {'git_sha': 'c452f562890534ca3d0a331de7c35b744037fdae'}, 'mash/sketch': {'git_sha':                                       
         'e745e167c1020928ef20ea1397b6b4d230681b4d'}, 'merquryfk/katcomp': {'git_sha': '280eec531785bdba28faf01bd6dd6b41fabccb8e'}, 'merquryfk/katgc': {'git_sha':                             
         '233fa70811a03a4cecb2ece483b5c8396e2cee1d'}, 'merquryfk/merquryfk': {'git_sha': '8ded6d441abe1a111c20482fa50ad3837b1747bf'}, 'merquryfk/ploidyplot': {'git_sha':                      
         '0af6adef555e54c2dcf0343646325864cacb5176'}, 'meryl/count': {'git_sha': 'a43bc940d6aaeaa755b34484cffeb5b41bce92eb'}, 'meryl/histogram': {'git_sha':                                   
         '129f57ccd9adc9016aaa3f2e2e6ab556ba8de7b6'}, 'meryl/unionsum': {'git_sha': '57fee2b3d6759c36f2a3e9181ab5f309cf62b6f1'}, 'minimap2/align': {'git_sha':                                 
         '1a5a9e7b4009dcf34e6867dd1a5a1d9a718b027b'}, 'quast': {'git_sha': 'd473a247d2e0c619b0df877ea19d9a5a98c8e3c8'}, 'samtools/fastq': {'git_sha':                                          
         '897c33d5da084b61109500ee44c01da2d3e4e773'}, 'seqkit/split2': {'git_sha': 'e745e167c1020928ef20ea1397b6b4d230681b4d'}} does not have a git_url or modules entry                       
INFO     The 'modules.json' file is not up to date. Recreating the 'module.json' file.                                                                                      modules_json.py:439
INFO     Was unable to find matching module files in the master branch.                                                                                                     modules_json.py:231
? Was the modules installed from a different branch in the remote? No
ERROR    Branch 'No' not found in 'nf-core/modules'                                                                                                                             __main__.py:540
System information

The environment is the Gitpod environment where:

  • nextflow -version: version 22.04.0 build 5697
  • Hardware: Cloud
  • OS: Unix
  • version of nf-core tools: 2.5.1
  • Python 3.9.12

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