John Sundh

Fewer assignments when reference has more taxonomic labels

3

Hi! We're trying to benchmark assignTaxonomy together with some other tools for taxonomic classification of ASVs. In doing so we ran assignTaxonomy with 1000 test sequences against 3 versions of...

Conda verification error when installing krona on OSX

4

I'm trying to install krona from conda but the installation fails on the `Verifying transaction:` step due to missing files specified in the manifest: >CondaVerificationError: The package for krona located...

An error occurred while retrieving available packages

5

## Description I'm getting an error message saying "An error occurred while retrieving available packages" as well as "I know you want to give up, but wait a bit longer.."...

Describe your pull request here ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). ### General instructions * If this PR adds or updates a...

Vertical integration of datasets

3

Thanks for a great package and very useful publications! I'm working with a time-series of samples for which metagenomic (`mg`) and metatranscriptomic (`mt`) data has been generated using Illumina sequencing....

Facilitate distribution via updated Dockerfile and repo structure

2

**Is your feature request related to a problem? Please describe.** It would be great to be able to incorporate an `stpipeline` container in workflows (_e.g._ Snakemake or Nextflow). As it...

Wrong input file passed to barcodeDemultiplexing

2

**Describe the bug** When running with `--disable-mapping` the pipeline passes the "quality_trimmed_R2" file as input to `barcodeDemultiplexing` instead of existing `mapped.bam` file in output directory. This causes pysam to throw...

Hi, I'm running a correlation/proportionality analysis on a multiomic dataset (metagenomic, metatranscriptomic and metaproteomic). I'm trying to correlate features in one dataset to the same features in one of the...