Weird folder with Biocontainers JSON file

[hansioan]

@hmenager @osallou Hi guys,

There is a folder: https://github.com/bio-tools/content/tree/master/data/CCMetagen

with a file called https://github.com/bio-tools/content/blob/master/data/CCMetagen/biocontainers.biotools.json

which is not a bio.tools file, I assume this CCMetagen folder, which is different from https://github.com/bio-tools/content/tree/master/data/ccmetagen

is just some folder that got left behind. Do we need this? I'm also asking because it contains the file with the name biocontainers.biotools.json which is the naming convention for bio.tools files.

Thanks, Hans

[osallou]

@hmenager seems you renamed this file Biocontainers, via auto PR, adds a biocontainers.json file. Should we modify our CI to inject biocontainers.biotools.json file instead?

[hansioan]

Please don't add files that end in .biotools.json Those should only be files from bio.tools annotations. The convention we have is that we have the folder names the same as the tool ids and the files have the same name + the specific extension, e.g.:

For tool id blast Folder is data/blast Files are:

• data/blast/blast.biotools.json
• data/blast/blast.debian.yaml

See more files like this at: https://github.com/bio-tools/content/tree/master/data/blast

I think a biocontainers.json file should be fine, but not biocontainers.biotools.json. The problem came up because the file was called biocontainers.biotools.json

[hmenager]

I was the one who made that mistake, ironically enough this was while I was trying to enforce the rules you mention @hansioan.

[hmenager]

this is, as far as I understand, the only "erroneous" file at this stage in the repository:

• CCMetagen/biocontainers.biotools.json

I suggest I rename it to ccmetagen/ccmetagen.biocontainers.json. Is that fine with you @hansioan ? @osallou ?

[osallou]

all our files are biocontainers.json , so best if possible is to keep same naming

[hmenager]

ok, it sounds reasonable to keep the names this way then. Out of curiosity @osallou, where are these files stored on the biocontainers side? Is this a repo somewhere? And how/at which frequency are they updated?

[osallou]

They are not on our side, in biocontainers CI we create a PR with new/updated tools based on our metadata