jhuapl-bio/taxtriage

Issues

• Returned top hits from distributions against expected is too large

  #69 opened 2 months ago by Merritt-Brian
  0

• Add Save Unaligned for Minimap2 and Bowtie2

  #66 opened 2 months ago by Merritt-Brian
  0

• Porechop causes workflow to fail if nothing trims from a sample

  #58 opened 3 months ago by Merritt-Brian
  2

• Add Centrifuge and metaPhlan2

  #27 opened a year ago by Merritt-Brian
  4

• Pathogens not reported as pathogen in report

  #63 opened 5 months ago by Merritt-Brian
  1

• conflicting licenses in the repo

  #62 opened 6 months ago by romerocesar
  1

• Use local Refseq mirror for post-kraken2 accession querying

  #61 opened 6 months ago by Merritt-Brian
  0

• Add Kaiju classification approach

  #30 opened 7 months ago by Merritt-Brian
  0

• Breadth (X) of Coverage Column no longer works with aggregate assembly alignment

  #48 opened 8 months ago by Merritt-Brian
  1

• Pipeline fails at Porechop step

  #55 opened 8 months ago by poojasgupta
  10

• Add a Primary report file that is a single, simple table. Make the full multiqc file supplemental

  #51 opened 9 months ago by Merritt-Brian
  1

• Conda Integrated

  #53 opened 9 months ago by Merritt-Brian
  0

• RE-implement BLAST refinement strategies

  #24 opened 9 months ago by Merritt-Brian
  0

• NanoPlot fails for the test config files - Singularity Only

  #52 opened 9 months ago by Merritt-Brian
  1

• Adding Submodule - Gene prediction and annotation for mapped reads

  #42 opened 9 months ago by Merritt-Brian
  2

• bin/merge_assemblies_conf.py assumes file content, no QA check

  #50 opened 9 months ago by chrisgulvik
  2

• Add Minmapq filter to samtools

  #47 opened 9 months ago by Merritt-Brian
  1

• Add Submodule - Samtools Coverage Histogram File

  #46 opened 9 months ago by Merritt-Brian
  1

• Remove the split VCF by contig

  #49 opened 9 months ago by Merritt-Brian
  0

• Aggregate Multi Contig/Accession/Chromosome Stats per Sample & Taxa

  #41 opened 10 months ago by Merritt-Brian
  0

• Retry NCBI Reference Pulls

  #40 opened 10 months ago by Merritt-Brian
  0

• Workflow didn't finish

  #45 opened 10 months ago by erinyoung
  11

• top_hits.nf seems to have wrong number of arguments

  #28 opened 10 months ago by hkunerth
  8

• There are log of warning and channel.view() lines that get printed to the screen while running.

  #44 opened a year ago by erinyoung
  1

• Add Nanoplot/Fastq as outputs to Tower YAML file

  #34 opened a year ago by Merritt-Brian
  0

• Add preliminary step: Host Removal via Alignment

  #33 opened a year ago by Merritt-Brian
  1

• confidences.merged_mqc.tsv does not incorporate into the MultiQC

  #22 opened a year ago by gunarsosis
  4

• Improvement: Speed of SPLIT_VCF

  #20 opened a year ago by Merritt-Brian
  1

• Split up the acc and index columns for the kraken report and confidence report

  #18 opened a year ago by Merritt-Brian
  0

• Confidence Metrics fails for tsv files with mismatched column count

  #16 opened a year ago by Merritt-Brian
  0

• Stats and Assembly Runs only on LCA Species Level from Kraken2 filtered reads

  #17 opened a year ago by Merritt-Brian
  0

• Unmapped variable "ch_spades_hmm"

  #8 opened a year ago by hkunerth
  2

• Issue running TaxTriage in basestack

  #6 opened a year ago by garfinjm
  9