Pathogen-Genomics-Cymru/lodestone

Issues

• Bovis miscategorised as MTB

  #104 opened 3 months ago by WhalleyT
  3

• If only one VCF is created (or populated) ignore Cortex

  #105 opened 3 months ago by WhalleyT
  0

• New references

  #103 opened 3 months ago by WhalleyT
  0

• Assembly

  #64 opened 3 months ago by WhalleyT
  1

• TB-profiler report

  #75 opened 3 months ago by WhalleyT
  3

• tb-profiler collate

  #97 opened 3 months ago by WhalleyT
  0

• G1 (species complex) missing in Kraken2

  #89 opened 3 months ago by WhalleyT
  1

• Iteratively loop through contaminant removal

  #65 opened 3 months ago by WhalleyT
  2

• Thresholding issues

  #76 opened 3 months ago by WhalleyT
  0

• Permissive flag on decontamination

  #86 opened 3 months ago by WhalleyT
  2

• 0.98a checklist

  #88 opened 3 months ago by WhalleyT
  0

• TB-profiler new issue

  #62 opened 3 months ago by MarcNiebel
  4

• FTP issues

  #87 opened 3 months ago by WhalleyT
  1

• Flag to download assembly

  #90 opened 3 months ago by WhalleyT
  0

• Hanging recursion

  #85 opened 3 months ago by WhalleyT
  0

• Process:summarise: identify_tophit_and_contaminants2.py KeyError

  #63 opened 4 months ago by WhalleyT
  2

• stub runs

  #60 opened 4 months ago by WhalleyT
  1

• assembly_summary_refseq.txt :check for updates or go straight to wget file

  #70 opened 4 months ago by WhalleyT
  2

• Threshold decontamination

  #72 opened 4 months ago by WhalleyT
  0

• use https links rather than ftp

  #69 opened 4 months ago by WhalleyT
  1

• Missing version for tb-profiler container

  #66 opened 5 months ago by WhalleyT
  1

• Tb-profiler issue

  #58 opened 5 months ago by MarcNiebel
  6

• intracellulare when statement bug

  #54 opened 5 months ago by annacprice
  3

• TB-profiler issue v2

  #61 opened 5 months ago by MarcNiebel
  13

• Singularity permissions error

  #53 opened 5 months ago by annacprice
  3

• Spython

  #59 opened 5 months ago by WhalleyT
  0

• Update TB profiler manually

  #56 opened 7 months ago by WhalleyT
  1

• Additions for v0.9.8

  #49 opened 9 months ago by annacprice
  1

• Minos fails when trying to compare against an empty VCF file

  #35 opened 10 months ago by WhalleyT
  4

• Empty contaminated.fa and failed in preprocessing:mapToContamFa process

  #17 opened a year ago by alantsangmb
  8

• Unable to analyze single FASTQ reads

  #42 opened a year ago by idolawoye
  1

• Bowtie2 database

  #37 opened 2 years ago by khoahoc0508
  0

• preprocessing:identifyBacterialContaminants is identifying human reads as a contaminant to remove

  #21 opened 2 years ago by annacprice
  2

• Update identify_tophit_and_contaminants2.py to reflect the new NCBI taxonomy

  #15 opened 2 years ago by annacprice
  2

• Add missing report generation to preprocessing:summarise

  #16 opened 2 years ago by annacprice
  2

• species hits from Afanc missing dot abbreviations

  #18 opened 2 years ago by annacprice
  2

• Samples not passing to clockwork

  #22 opened 2 years ago by annacprice
  2

• Samples not passing to gnomonicus

  #26 opened 2 years ago by annacprice
  2

• Scripting/reporting still referring to mykrobe when it should refer to afanc

  #31 opened 2 years ago by annacprice
  2

• Error in read counting in preprocessing:fastp

  #32 opened 2 years ago by annacprice
  2

• Bash variables not being substituted in json

  #33 opened 2 years ago by annacprice
  2

• Empty contaminants.fa in preprocessing:downloadContamGenomes

  #20 opened 2 years ago by annacprice
  2

• AttributeError: 'list' object attribute 'append' is read-only in bin/create_final_json.py

  #27 opened 2 years ago by WhalleyT
  1

• Resource request in nextflow.config not working

  #19 opened 2 years ago by annacprice
  0

• changes needed for vcfpredict sub-workflow

  #12 opened 2 years ago by annacprice
  1

• samtools sort error in clockwork:alignToRef

  #4 opened 2 years ago by annacprice
  3

• Some samples don’t pass to clockwork when unmix_myco is set to yes

  #11 opened 2 years ago by annacprice
  1

• Need to pin version of clockwork in container

  #9 opened 2 years ago by annacprice
  1

• Read pair counting bug in preprocessing:fastp

  #6 opened 3 years ago by ArthurVM
  0

• clockwork:callVarsMpileup writing files outside working directory

  #3 opened 3 years ago by annacprice
  1