Publication figures and questions General Describe datasets (samples, contig number + size, file size) Pipeline overview Describe run time + resources Maybe: give run time for different resource constellations Report/compare results of all tools (e.g. Venn diagrams) Which antibiotics/secondary metabolites are in (meta)genomes? :arrow_right: Targeted ARG/BGC identification

Methods: Bioinformatic ARG detection on assembled sequences Characterization of antimicrobial resistance genes and virulence factor genes in an Arctic permafrost region revealed by metagenomics (2021, Environmental Pollution)ORF prediction (MetaGeneAnnotator with default parameters) ORF clustering (90% coverage using CD-HIT, representative sequence = longest sequence per cluster) ARG prediction: Align cluster representatives against CARD using DIAMOND BLASTP. Taxonomic assignments: Align cluster representatives against NCBI non-redundant protein sequences database NR using DIAMOND. Reduce false positives by stringent thresholds: E-value <1e+5, identity > 70%, alignment length >50 Normalization/gene abundance: Transcripts per million (TPM) calculated via Kallisto and merged with alignment results via contig ID. MGE prediction: AMR module of PathoFact pipeline Identify potential PARBs (pathogenic ABR bacteria): bin contigs into MAGs (MetaBAT 2 and MaxBin 2 from the MetaWRAP pipeline) and map ARGs onto them (in a seems-like unnecessarily laborious process...). Statistics on dataset parameters in R(e.g. physiochemical parameters (pH...); for our samples maybe age, geographic location, origin (dental calculus, paleofeces...), host species...

Modules / subworkflows spring cleaning march 2023 Tasks Assign "stale" labels and comment the following message to all PRs and issues older than 1 year.Hi there!We've noticed there hasn't been much activity here. Are you still planning on working on this? If not, you can ignore this message and we'll close your PR/Issue in about 2 weeksCheers the nf-core maintainersImportant: If PR/issue looks relevant, we can keep it for the hackathon (tag: hackathon2023 or good_first_issue). If still present after the hackathon without further comments, we delete it. Standardize meta.yml keywords: the left sidebar on https://nf-co.re/modules is very long and repetitive if tags are written with slight differences Review and merge open PRs Review open branches Task distribution

Developing FuncScan  We are a nf-core pipeline! :raised_hands: Evolution of the workflow A bunch of tools to detect... ARGs – Antibiotic resistance genes AMPs – Antimicrobial peptides