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Nextflow output shows this message for failed runsnp job:
``[2e/4888ce] NOTE: Process `STANDARD_AMRplusplus_wKraken:FASTQ_RESISTOME_WF:runsnp (NS.1508.003.IDT_i7_165---IDT_i5_165.COR05e_t2_M)\` termi…
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Add scripts and documentation for calculating the resistome
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hello, i want to ask if the pipeline is suited for HiFi reads? or should I treat every HiFi read as single genome and use this pipeline in genome method.
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Using a local eda backend setup, noticed that in the Resistome-1 study the wgs variables are missing.
Sent: GET request to `http://localhost:8080/studies/Resistome-1` (local subsetting service)
…
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This is about adjusting the sample details mapping in the new .owl so I can use it for EDA data loading.
Because EDA allows an entity graph, we no longer need separate studies for different result …
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Hi,
I am running Nullarbor on a Singularity based container system and I have run this numerous times using make preview and eliminated any possible contaminants. I have also used seqtk sample to …
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The tools "SNPFinder" (https://usegalaxy.no/root?tool_id=toolshed.g2.bx.psu.edu/repos/chrisd/snpfinder/snpfinder/0.1.0), "RarefactionAnalyzer" (https://usegalaxy.no/root?tool_id=toolshed.g2.bx.psu.edu…
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This is less of an issue and more of a warning to other users. I am using the conda build of rgi v5.2.0 to annotate resistance genes in metaSPAdes contigs. The [instructions on loading the reference…
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Hi,
The pipeline completes and generates the html report however the resistome and virulome data is not displaying. The data is generated but it does not appear to be in the final resistome.csv thoug…
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Hey sraX devs,
I'm trying to run this on a file `contigs.fasta` using the following commands:
```
conda create –name sraX
conda activate sraX
sraX –v ## indicates successful install
## n…