mapseq_otu_krona sourcing krona/ktimporttext from nf-core

[vagkaratzas]

No description provided.

[chrisAta]

Looks good to me, but having a further look at the MAPseq module I remember that the developers released a patch to the newest version that makes the output deterministic. The amplicon pipeline already uses that version, see here: https://github.com/EBI-Metagenomics/amplicon-pipeline/blob/f189b2619c47fbb42655cda25b3cc7f9e08f6f14/modules/ebi-metagenomics/mapseq/main.nf#L6-L9

I think I forgot to change the conda container version but otherwise it should be mapseq:2.1.1b. Do you think you could update this too? That way this desync never happens again haha

[vagkaratzas]

Looks good to me, but having a further look at the MAPseq module I remember that the developers released a patch to the newest version that makes the output deterministic. The amplicon pipeline already uses that version, see here: https://github.com/EBI-Metagenomics/amplicon-pipeline/blob/f189b2619c47fbb42655cda25b3cc7f9e08f6f14/modules/ebi-metagenomics/mapseq/main.nf#L6-L9

I think I forgot to change the conda container version but otherwise it should be mapseq:2.1.1b. Do you think you could update this too? That way this desync never happens again haha

On it. I'll do it in this PR..just changing the conda and docker containers

[vagkaratzas]

@mberacochea @chrisAta the schema that is defined in the modules folder is different to the one that nf-core is checking with nf-core tools. So I cannot debug the error I am afraid. EIther we need to update the schema in the repo (probably all modules will complain afterwards though), or bypass the json schema linting, or you can fix if you know what's wrong :P

[chrisAta]

not done yet but noticed this real quick

[chrisAta]

@mberacochea @chrisAta the schema that is defined in the modules folder is different to the one that nf-core is checking with nf-core tools. So I cannot debug the error I am afraid. EIther we need to update the schema in the repo (probably all modules will complain afterwards though), or bypass the json schema linting, or you can fix if you know what's wrong :P

I just tried and ended up in the same death loop you did 💀 not sure what we should do? @mberacochea

[mberacochea]

.. unless @chrisAta has any objections

[chrisAta]

omg so happy to see this fixed now, thanks @mberacochea !!