Joon-Klaps/viralgenie

Issues

• Contig consensus 0 coverage

  #110 opened 2 months ago by Joon-Klaps
  1

• Filtering clusters

  #136 opened 3 months ago by Joon-Klaps
  1

• Make custom annotation database using ncbi virus

  #137 opened 3 months ago by Joon-Klaps
  0

• include option for protein clustering

  #135 opened 3 months ago by Joon-Klaps
  0

• Include coverage plot in MQC

  #113 opened 5 months ago by Joon-Klaps
  1

• Set default UMI-tools dedup strategy to a non-read counting method

  #120 opened 4 months ago by Joon-Klaps
  0

• FIx OOM for long contigs

  #124 opened 4 months ago by Joon-Klaps
  0

• Include sspace & cobra for contig extension

  #119 opened 4 months ago by Joon-Klaps
  0

• Vazymolo

  #121 opened 4 months ago by Joon-Klaps
  0

• Make a quick start section

  #122 opened 4 months ago by Joon-Klaps
  0

• Keep failed consensus contigs in qc alignment

  #66 opened 9 months ago by Joon-Klaps
  0

• Refactor splitting up parts for cleaner code

  #78 opened 8 months ago by Joon-Klaps
  0

• patch nf-core modules

  #116 opened 5 months ago by Joon-Klaps
  0

• patch nf-core template

  #115 opened 5 months ago by Joon-Klaps
  0

• nf-test

  #114 opened 5 months ago by Joon-Klaps
  0

• Don't pipe number of members in file name

  #28 opened a year ago by Joon-Klaps
  1

• Check Why singletons are no longer supported

  #34 opened a year ago by Joon-Klaps
  0

• Report contigs with less then minimum X

  #26 opened a year ago by Joon-Klaps
  0

• Refactor readclassifier & preclustering

  #95 opened 5 months ago by Joon-Klaps
  1

• Deduplicate UMI's at fastq level

  #27 opened 5 months ago by Joon-Klaps
  2

• Simplify preclustering of contigs up to a certain level

  #90 opened 5 months ago by Joon-Klaps
  1

• Migrate annotation files to external repo

  #93 opened 5 months ago by Joon-Klaps
  1

• Interpretabilty output

  #72 opened 5 months ago by Joon-Klaps
  0

• Identify total number of reads after host-removal not just %

  #85 opened 5 months ago by Joon-Klaps
  1

• Out-of-memory during NETWORK_CLUSTER process on unclassified taxa

  #105 opened 5 months ago by sheerenbiol
  0

• Catching of samples with no contigs to identify a reference against a database

  #65 opened 6 months ago by Joon-Klaps
  1

• autodetect paired-end

  #102 opened 6 months ago by Joon-Klaps
  0

• Constrained sequence header edit

  #58 opened 6 months ago by Joon-Klaps
  2

• Update docs & make release

  #61 opened 6 months ago by Joon-Klaps
  0

• Implement samplesheet support for mapping constrains

  #49 opened 7 months ago by Joon-Klaps
  1

• Include option to remove files if pipeline did not complete

  #75 opened 7 months ago by Joon-Klaps
  0

• Annotate final contigs with species AND segment name

  #73 opened 7 months ago by Joon-Klaps
  2

• Incude used tools in sample table

  #50 opened 10 months ago by Joon-Klaps
  1

• Difference in depth bcftools mpileup vs samtools mpileup

  #84 opened 7 months ago by Joon-Klaps
  2

• Make a conda biocontainer for viralgenie

  #88 opened 8 months ago by Joon-Klaps
  0

• Blast result include complete sequence title

  #74 opened 8 months ago by Joon-Klaps
  0

• Multiqc report for quast include assemblers

  #67 opened 8 months ago by Joon-Klaps
  1

• Include Krona report generation

  #64 opened 8 months ago by Joon-Klaps
  0

• Kaiju identifying the species but not reporting the species

  #62 opened 8 months ago by Joon-Klaps
  0

• Sanity check failed

  #55 opened 8 months ago by Joon-Klaps
  3

• Convert reference pool

  #56 opened 8 months ago by Joon-Klaps
  0

• Explore capabalities of COMEBin

  #80 opened 8 months ago by Joon-Klaps
  0

• Consensus calling without reference bias if contig is constructed

  #63 opened 9 months ago by Joon-Klaps
  0

• Global prefix for results

  #68 opened 9 months ago by Joon-Klaps
  1

• Maskbed fasta incorrect input

  #57 opened 9 months ago by Joon-Klaps
  0

• Kraken2 contig annotation

  #20 opened 9 months ago by Joon-Klaps
  1

• Kraken2 for host & contamination removal

  #40 opened 9 months ago by Joon-Klaps
  1

• Consider implementing vRhyme

  #29 opened 10 months ago by Joon-Klaps
  1

• Update Member and centroid extraction

  #23 opened a year ago by Joon-Klaps
  0

• Trinity fails when dealing with very few reads

  #21 opened a year ago by Joon-Klaps
  1