Francisco Zorrilla

Error message raised in snakemake-workflow-catalogue

2

Hi, I searched for the [metaGEM](https://github.com/franciscozorrilla/metaGEM) workflow in the [snakemake catalogue](https://snakemake.github.io/snakemake-workflow-catalog/) and I see that the QC tab shows that my formatting is failing. Clicking on the failed formatting badge...

Hi Daniel, I have seen the following warning sometimes pop up during model reconstruction with CarveMe, complaining that gene association for certain reactions are not in disjunctive normal form (DNF)....

#159

feature: test and compare new binners

4

The binning landscape has changed since the initial development of metaGEM. It would be a good idea to get a shortlist of novel binning tools for testing, with the ultimate...

feature: test & enable bioconda installation on macbook

1

Would be great if users could conda install metagem locally on apple ARM architecture machines, initially suggested here #122 This is not meant for standard usage, but could be helpful...

# 🩻 Single batch submission of GTDBTk-based taxonomic classification 🚀 Current GTDBTk rule is great when dealing with many metagenomes, but when dealing with many isolate samples it makes more...

# 🥚 eggNOG-mapper for better functional annotation 🍸 ## 🐍 Snakefile tasks - [x] create eggnog-mapper rule for processing ORF-annotated protein fasta files of genomes - [ ] create helper/supplementary...

# 🦠 Isolate genomes subworkflow 🔦 Adding support for isolate genome assembly in the next version of metaGEM 💎 ## 🐍 Snakefile tasks - [x] create shovill rule for dealing...

improvement: use `wc` to count bp instead of summing contig header info for abundance

1

For abundance calculation we need to get bp of genome, currently we do this based on the contig headers info, although this can become problematic for genomes assembled by different...