nf-core/bacass

Issues

• Execution failed when --kmerfinder_db and --ncbi_assembly_metadata are provided

  #188 opened 21 days ago by IBEXCluster
  5

• FASTP module not finding input paths

  #187 opened a month ago by hazlemhub
  2

• Fix warning messages on process name

  #127 opened a month ago by Daniel-VM
  0

• MultiQC Input File Name Collision

  #185 opened a month ago by rvijay-seqcoast
  0

• Support of concatenation of multiple fastq files form the same sample

  #156 opened 2 months ago by Daniel-VM
  0

• Bakta running only for one sample

  #171 opened 2 months ago by SchwarzMarek
  5

• Update Unicycler to 0.5.1

  #177 opened 2 months ago by leppd
  1

• remove the need for `ncbi_assembly_metadata`

  #172 opened 3 months ago by SchwarzMarek
  1

• kmerfinder update and optimization

  #170 opened 3 months ago by SchwarzMarek
  7

• Error when ONT only + dragonflye + nanopolish

  #165 opened 3 months ago by SchwarzMarek
  1

• bacass does not run canu assebler when requested

  #164 opened 3 months ago by SchwarzMarek
  3

• save_merged discards the merged reads

  #161 opened 3 months ago by santiagorevale
  6

• Chack whether `--assembly_type` parameter is requiered in nextflow run and update `README.md`

  #144 opened 6 months ago by Daniel-VM
  0

• Migration from nf-validation to nf-schema

  #143 opened 6 months ago by Daniel-VM
  0

• MultiQC Version 1.21 Parsing Issue

  #142 opened 6 months ago by Daniel-VM
  0

• MultiQC doesn't include FastQC reports for trimmed reads

  #162 opened 3 months ago by santiagorevale
  5

• download_reference.py script can't find the top reference

  #155 opened 4 months ago by sralchemab
  10

• Feature request: allow directory paths for LongFastQ input

  #151 opened 6 months ago by watsonar
  2

• Update local/unicycler to nf-core/unicycler to Avoid Potential Versioning Issues

  #145 opened 6 months ago by Daniel-VM
  0

• samplesheet should have a suffix .tsv if it is a tab-separated file as described

  #64 opened 6 months ago by antunderwood
  8

• Improvements in forked repository: KmerFinder, Estimation of Reference Genome, Custom Quast, and Custom MultiQC Reports

  #109 opened 6 months ago by Daniel-VM
  3

• Prokka and Bakta are reporting single log in multiqc report when running multiple samples

  #132 opened 7 months ago by Daniel-VM
  0

• Running error of exit status 255

  #129 opened 8 months ago by aslangabriel99
  1

• Save trimmed parameter saying 'false' is not a valid choice

  #128 opened 8 months ago by rvijay-seqcoast
  2

• URGENT: pin nf-validation version

  #113 opened 8 months ago by nvnieuwk
  2

• Add flye to nf-core/bacass

  #115 opened 9 months ago by lborcard
  12

• Allow dragonflye to polish draft genome with short-reads

  #105 opened a year ago by Daniel-VM
  0

• List of ideas to improve assemblies

  #57 opened 3 years ago by d4straub
  9

• New module - dragonflye - for long-read assembly

  #101 opened a year ago by Daniel-VM
  0

• Update bakta to v1.8.2

  #102 opened a year ago by Daniel-VM
  0

• Removal of Prokka in favor of Bakta

  #94 opened a year ago by Daniel-VM
  3

• Enhance MultiQC to collect stats from all supported modules

  #92 opened a year ago by Daniel-VM
  0

• Local processes to nf-core/modules

  #61 opened 3 years ago by d4straub
  1

• Released nf-core v2.10 template

  #90 opened a year ago by Daniel-VM
  0

• nf-validation on sample sheet

  #87 opened a year ago by Daniel-VM
  3

• Working on updating the nf-core/tools template v2.9

  #85 opened a year ago by Daniel-VM
  2

• Single end Illumina processing?

  #82 opened 2 years ago by limey-bean
  1

• skewer.nf problem with Docker container.

  #78 opened 2 years ago by mbyott
  3

• Regex problem

  #71 opened 3 years ago by tiendu
  4

• Nanoplot expect png output in hybrid assembly mode

  #69 opened 3 years ago by jenmuell
  0

• Check for spaces in IDs in Sample Sheet

  #67 opened 3 years ago by ThHarbig
  1

• Add homopolish for nanopore-only assembly

  #66 opened 3 years ago by llk578496
  2

• Assembly Polishing is not working in the V2.0

  #63 opened 3 years ago by varunshamanna
  3

• sample sheet check reports wrong row item

  #65 opened 3 years ago by antunderwood
  1

• Can we access kraken2db from S3 bucket?

  #41 opened 3 years ago by piroonj
  4

• [Question] how to reduce Docker image size

  #50 opened 3 years ago by tamuanand
  1

• Unicycler version issue

  #51 opened 3 years ago by lch14forever
  4

• Conversion to DSL2 & update of tools

  #52 opened 3 years ago by d4straub
  2

• Documentation broken link

  #42 opened 3 years ago by danwiththeplan
  2

• Add back tests for kraken

  #37 opened 4 years ago by apeltzer
  2