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jhuapl-bio
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taxtriage
TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.
MIT License
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Updated pathogen sheet with non-human host viruses
#73
tasapl
closed
4 days ago
0
Multifasta - Allowing Directory or multiple files to be used for local FASTA
#72
Merritt-Brian
closed
1 week ago
0
Allow Multi FASTA input for `--reference_fasta` parameter
#71
Merritt-Brian
closed
1 week ago
1
Top Hits - Improper strain-level interpretations
#70
Merritt-Brian
closed
1 week ago
1
Returned top hits from distributions against expected is too large
#69
Merritt-Brian
opened
1 month ago
0
Phase3 merge to main
#68
Merritt-Brian
closed
1 month ago
1
Merge Minimap2 default to Stable
#67
Merritt-Brian
closed
1 month ago
0
Add Save Unaligned for Minimap2 and Bowtie2
#66
Merritt-Brian
opened
1 month ago
0
Refactoralignment merge for minimap2 default on short reads
#65
Merritt-Brian
closed
1 month ago
0
Merge Stable with Main
#64
Merritt-Brian
closed
1 month ago
0
Pathogens not reported as pathogen in report
#63
Merritt-Brian
closed
4 months ago
1
conflicting licenses in the repo
#62
romerocesar
closed
5 months ago
1
Use local Refseq mirror for post-kraken2 accession querying
#61
Merritt-Brian
opened
5 months ago
0
Merge to main to stable
#60
Merritt-Brian
closed
4 months ago
0
Merge multifasta update
#59
Merritt-Brian
closed
6 months ago
0
Porechop causes workflow to fail if nothing trims from a sample
#58
Merritt-Brian
closed
1 month ago
2
Merging Organisms and Top Hits into a single assembly pull, QoL Improvements
#57
Merritt-Brian
closed
7 months ago
0
Update pathogen table
#56
jdratcliff
closed
8 months ago
0
Pipeline fails at Porechop step
#55
poojasgupta
closed
7 months ago
10
Merge v1.3.2 into Stable branch
#54
Merritt-Brian
closed
8 months ago
0
Conda Integrated
#53
Merritt-Brian
opened
8 months ago
0
NanoPlot fails for the test config files - Singularity Only
#52
Merritt-Brian
opened
8 months ago
1
Add a Primary report file that is a single, simple table. Make the full multiqc file supplemental
#51
Merritt-Brian
closed
8 months ago
1
bin/merge_assemblies_conf.py assumes file content, no QA check
#50
chrisgulvik
closed
8 months ago
2
Remove the split VCF by contig
#49
Merritt-Brian
closed
9 months ago
0
Breadth (X) of Coverage Column no longer works with aggregate assembly alignment
#48
Merritt-Brian
closed
7 months ago
1
Add Minmapq filter to samtools
#47
Merritt-Brian
closed
9 months ago
1
Add Submodule - Samtools Coverage Histogram File
#46
Merritt-Brian
closed
9 months ago
1
Workflow didn't finish
#45
erinyoung
closed
9 months ago
11
There are log of warning and channel.view() lines that get printed to the screen while running.
#44
erinyoung
closed
10 months ago
1
NCBI Retry and Reference Download
#43
tasapl
closed
11 months ago
0
Adding Submodule - Gene prediction and annotation for mapped reads
#42
Merritt-Brian
closed
8 months ago
2
Aggregate Multi Contig/Accession/Chromosome Stats per Sample & Taxa
#41
Merritt-Brian
closed
9 months ago
0
Retry NCBI Reference Pulls
#40
Merritt-Brian
closed
9 months ago
0
Metaphlan
#39
tasapl
closed
8 months ago
0
allow clean fastq.gz
#38
Merritt-Brian
closed
1 year ago
0
Adding samtools coverage, skip failed genome pulls
#37
Merritt-Brian
closed
1 year ago
0
Merging Table Row Fix for max counts, updating NF Tower Configurations
#36
Merritt-Brian
closed
1 year ago
0
adding multiqc table rows max
#35
Merritt-Brian
closed
1 year ago
0
Add Nanoplot/Fastq as outputs to Tower YAML file
#34
Merritt-Brian
closed
12 months ago
0
Add preliminary step: Host Removal via Alignment
#33
Merritt-Brian
closed
12 months ago
1
Merge process memory needs
#32
Merritt-Brian
closed
1 year ago
0
Merge nf tower changes
#31
Merritt-Brian
closed
1 year ago
0
Add Kaiju classification approach
#30
Merritt-Brian
closed
6 months ago
0
Merge defaults
#29
Merritt-Brian
closed
1 year ago
0
top_hits.nf seems to have wrong number of arguments
#28
hkunerth
closed
9 months ago
8
Add Centrifuge and metaPhlan2
#27
Merritt-Brian
opened
1 year ago
4
Merging Main fixes
#26
Merritt-Brian
closed
1 year ago
0
Separate accession cols and create reports by rank
#25
tasapl
closed
1 year ago
0
RE-implement BLAST refinement strategies
#24
Merritt-Brian
closed
8 months ago
0
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