Comments (2)
This currently is implemented but cant take >80GB of RAM for general data. Not recommended. Use --skip_features
for now to disable this
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Completed in release https://github.com/jhuapl-bio/taxtriage/releases/tag/v1.3.0
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Related Issues (20)
- Add preliminary step: Host Removal via Alignment HOT 1
- Add Nanoplot/Fastq as outputs to Tower YAML file
- Retry NCBI Reference Pulls
- Aggregate Multi Contig/Accession/Chromosome Stats per Sample & Taxa
- There are log of warning and channel.view() lines that get printed to the screen while running. HOT 1
- Workflow didn't finish HOT 11
- Add Submodule - Samtools Coverage Histogram File HOT 1
- Add Minmapq filter to samtools HOT 1
- Breadth (X) of Coverage Column no longer works with aggregate assembly alignment HOT 1
- Remove the split VCF by contig
- bin/merge_assemblies_conf.py assumes file content, no QA check HOT 2
- Add a Primary report file that is a single, simple table. Make the full multiqc file supplemental HOT 1
- NanoPlot fails for the test config files - Singularity Only HOT 1
- Conda Integrated
- Pipeline fails at Porechop step HOT 10
- Porechop causes workflow to fail if nothing trims from a sample
- Use local Refseq mirror for post-kraken2 accession querying
- conflicting licenses in the repo HOT 1
- Pathogens not reported as pathogen in report
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