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Right now, assembly groups are a user-input parameter.
## Background
- Deciding which samples should be assembled together is difficult. Co-assembly of multiple samples can improve recovery of ass…
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## Description
Negative controls require all reads linked to their housekeeper bundle and have the read counts added to the sample in statusdb and LIMS.
## Suggested solution
~~When we parse …
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# P12002 Duplicated Reads
Inspecting the FastQC and MultiQC reports.
## Overrepresented and duplicated sequences
There are four samples (**_117, _145, _177, _187) that have high sequence duplicat…
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### Description of feature
As one of the input database files (silva_species_assignment_v138.1.fa.gz) stores an information about the 16S gene primary accession in GenBank database, I'm looking for t…
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Biosamples are normally from a tissue sample that can be named. This data should be represented as a named field of a Biosample message, i.e. `tissue_type`. I suppose one might use something like the …
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As per assembly workflow in Really Quick Copy-And-Paste Quick Start I copied the json file specified and execute the following which gave me the following error:
$ export SINGULARITY_BINDPATH="data:…
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Please post below to request a review.
### TODO
* [ ] some example workflow
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### Operating System
Windows 10
### Other Linux
_No response_
### Workflow Version
v24.04.2
### Workflow Execution
Command line (Cluster)
### Other workflow execution
_No response_
### EPI2M…
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### Description of the bug
Dear colleagues,
I have a question similar to that https://github.com/nf-core/viralrecon/issues/198 when trying to launch test experiment.
nextflow \
run nf-core/viralre…
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It’s sort of difficult to keep pace with all your different releases😀. So, which one should I use? Kraken, KrakenUniq or centrifuge??? I just have started centrifuge; should I move to KrakenUniq?
T…