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Seems there are some incompatibilities at the moment regarding MetaPhlAn, StrainPhlAn and HUMAnN. Now seems like a good time to issue an update together with the new releases of version 3 for all afor…
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## Bug report
### Expected behavior and actual behavior
The fromSRA channel factory method should give back a channel with tuples containing the accession number and corresponding ftp link/fast…
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Hey, I got this question and I don't know how to answer it, so I'm passing it on to you. Since it's code-related, I've made it an issue:
"Do you know why they are including `--merged` in the DeDup co…
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### branch
`158-biobakery-update` was used, however these sections were unmodified so the problem is likely present in `master` branch as well
### config
```
#########################
# Pipelin…
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Hi!
I am trying to run the Taxonomic-Functional-Profiling-Protein pipeline, but there seems to be an error during the sam2rma step.
**This is the command I am using**:
snakemake --snakefile Snak…
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Dear Francisco,
Recently, I have tried to use your pipeline to analyse some metagenome data. For the bin, i found I can only get about 30 MAGs of high quality (completeness > 90% by checkM). So I am …
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I think it is time to review the BACTpipe workflow and update/replace some parts.
Looking for input @huyue87 and @thorellk!
I have the following ideas:
- Remove `mash screen` (#54). It was o…
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Hi, I want to analysis some metagenome data using metaphlan3. But the result only contain bacteria. It seems like full_chocophlan.v296_201901.tar.gz only contain 10669 bacteria fnn files. Is this ture…
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Similar to FASTA and MultiFASTA, there are two acceptable profiling formats:
1. Those that contain a single profile (like [this example](https://github.com/dkoslicki/CAMIProfilingVisualization/blob…
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per #1159