A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

I'm using magmap 1.2.0 to map my shotgun metagenomes back to a small set of custom reference assemblies (using the genomeinfo argument). Is there a way to break down the mapping coverage by reference name rather than just overall for each sample? I don't see that particular break down in any of the files in summary_tables.

There isn't any finished table for that, but it's easy to do e.g. in R:
```library(tidyverse)
read_tsv('results/summary_tables/magmap.CDS.counts.tsv.gz') %>%
  group_by(accno, sample) %>%
  summarise(counts = sum(counts), tpm = sum(tpm), .groups = 'drop')```
That would give you numbers for CDS only of course.
If you'd find a finished table useful, we'd welcome an issue or, even better, a PR.

Bonus question: I get how TPM is calculated from the docs, but what does TPM stand for?

Transcripts Per Million. We should spell that out.