jhuapl-bio taxtriage issues

jhuapl-bio / 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

18 stars 4 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Pathogens not reported as pathogen in report

#63 Merritt-Brian closed 2 months ago
1
conflicting licenses in the repo

#62 romerocesar closed 3 months ago
1
Use local Refseq mirror for post-kraken2 accession querying

#61 Merritt-Brian opened 3 months ago
0
Merge to main to stable

#60 Merritt-Brian closed 2 months ago
0
Merge multifasta update

#59 Merritt-Brian closed 4 months ago
0
Porechop causes workflow to fail if nothing trims from a sample

#58 Merritt-Brian opened 5 months ago
1
Merging Organisms and Top Hits into a single assembly pull, QoL Improvements

#57 Merritt-Brian closed 5 months ago
0
Update pathogen table

#56 jdratcliff closed 6 months ago
0
Pipeline fails at Porechop step

#55 poojasgupta closed 5 months ago
10
Merge v1.3.2 into Stable branch

#54 Merritt-Brian closed 6 months ago
0
Conda Integrated

#53 Merritt-Brian opened 6 months ago
0
NanoPlot fails for the test config files - Singularity Only

#52 Merritt-Brian opened 6 months ago
1
Add a Primary report file that is a single, simple table. Make the full multiqc file supplemental

#51 Merritt-Brian closed 6 months ago
1
bin/merge_assemblies_conf.py assumes file content, no QA check

#50 chrisgulvik closed 6 months ago
2
Remove the split VCF by contig

#49 Merritt-Brian closed 6 months ago
0
Breadth (X) of Coverage Column no longer works with aggregate assembly alignment

#48 Merritt-Brian closed 5 months ago
1
Add Minmapq filter to samtools

#47 Merritt-Brian closed 6 months ago
1
Add Submodule - Samtools Coverage Histogram File

#46 Merritt-Brian closed 6 months ago
1
Workflow didn't finish

#45 erinyoung closed 7 months ago
11
There are log of warning and channel.view() lines that get printed to the screen while running.

#44 erinyoung closed 8 months ago
1
NCBI Retry and Reference Download

#43 tasapl closed 9 months ago
0
Adding Submodule - Gene prediction and annotation for mapped reads

#42 Merritt-Brian closed 6 months ago
2
Aggregate Multi Contig/Accession/Chromosome Stats per Sample & Taxa

#41 Merritt-Brian closed 7 months ago
0
Retry NCBI Reference Pulls

#40 Merritt-Brian closed 7 months ago
0
Metaphlan

#39 tasapl closed 6 months ago
0
allow clean fastq.gz

#38 Merritt-Brian closed 10 months ago
0
Adding samtools coverage, skip failed genome pulls

#37 Merritt-Brian closed 10 months ago
0
Merging Table Row Fix for max counts, updating NF Tower Configurations

#36 Merritt-Brian closed 10 months ago
0
adding multiqc table rows max

#35 Merritt-Brian closed 10 months ago
0
Add Nanoplot/Fastq as outputs to Tower YAML file

#34 Merritt-Brian closed 10 months ago
0
Add preliminary step: Host Removal via Alignment

#33 Merritt-Brian closed 10 months ago
1
Merge process memory needs

#32 Merritt-Brian closed 10 months ago
0
Merge nf tower changes

#31 Merritt-Brian closed 10 months ago
0
Add Kaiju classification approach

#30 Merritt-Brian closed 4 months ago
0
Merge defaults

#29 Merritt-Brian closed 11 months ago
0
top_hits.nf seems to have wrong number of arguments

#28 hkunerth closed 7 months ago
8
Add Centrifuge and metaPhlan2

#27 Merritt-Brian opened 11 months ago
4
Merging Main fixes

#26 Merritt-Brian closed 11 months ago
0
Separate accession cols and create reports by rank

#25 tasapl closed 11 months ago
0
RE-implement BLAST refinement strategies

#24 Merritt-Brian closed 6 months ago
0
changed singularity container to include wget https support

#23 gunarsosis closed 11 months ago
1
confidences.merged_mqc.tsv does not incorporate into the MultiQC

#22 gunarsosis closed 10 months ago
4
merge main v1.01 stable

#21 Merritt-Brian closed 11 months ago
0
Improvement: Speed of SPLIT_VCF

#20 Merritt-Brian closed 10 months ago
1
Merge main to stable

#19 Merritt-Brian closed 1 year ago
0
Split up the acc and index columns for the kraken report and confidence report

#18 Merritt-Brian closed 10 months ago
0
Stats and Assembly Runs only on LCA Species Level from Kraken2 filtered reads

#17 Merritt-Brian closed 11 months ago
0
Confidence Metrics fails for tsv files with mismatched column count

#16 Merritt-Brian closed 11 months ago
0
Merge Main to Stable

#15 Merritt-Brian closed 1 year ago
0
adding

#14 Merritt-Brian closed 1 year ago
0