Updating the modules.json file to new format results in branch lookup error
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@mirpedrol is already working on this.
Since Sep 20, 2022.
bug
- Dominant language
- Python
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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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