polio-nanopore/piranha

Issues

• default depth threshold has changed from 50 to 20?

  #260 opened 2 months ago by cathrnbp
  0

• subthreshold analysis if same. epid is flagged as positive in another sample

  #259 opened 2 months ago by aineniamh
  0

• flag if same epid and check for concurrence

  #258 opened 2 months ago by aineniamh
  0

• orange flag intermediate read counts

  #257 opened 2 months ago by aineniamh
  0

• other platforms check

  #256 opened 2 months ago by aineniamh
  0

• check if html table can be editable with pass and fail col

  #255 opened 2 months ago by aineniamh
  0

• put sample type in header- stool, es, isolate

  #254 opened 2 months ago by aineniamh
  0

• haplotyping probability pipeline with zoe's prototype

  #253 opened 2 months ago by aineniamh
  0

• demultiplexing as part of piranha- reducks?

  #252 opened 2 months ago by aineniamh
  0

• change default in percent to 0

  #251 opened 2 months ago by aineniamh
  0

• unit tests

  #250 opened 2 months ago by aineniamh
  0

• pick out relevant seqs of a certain distance and build subtrees

  #249 opened 2 months ago by aineniamh
  0

• add in pass/fail col and include in the sequence name too

  #248 opened 2 months ago by aineniamh
  0

• Ev reads present?

  #229 opened 3 months ago by Ceres90
  8

• Error during consensus building v1.2.3

  #236 opened 4 months ago by CatherineTroman
  8

• Error in rule generate_consensus_sequences V1.3

  #244 opened 4 months ago by jeroencremer
  1

• Semicolon as separator in barcodes.csv

  #235 opened 8 months ago by ebujaki
  1

• check percentage flag is getting applied

  #247 opened 4 months ago by aineniamh
  2

• videos describing how to use piranha

  #246 opened 4 months ago by aineniamh
  0

• lineage assignment for pv detected samples

  #245 opened 4 months ago by aineniamh
  0

• end extension by bam meddling? alt mapper either

  #232 opened 4 months ago by aineniamh
  1

• EPI2ME Desktop Use

  #221 opened 4 months ago by Ceres90
  9

• Error in rule generate_consensus_sequences V1.2.1, V1.2.5

  #242 opened 5 months ago by jeroencremer
  9

• implement maskara for npevs

  #231 opened 5 months ago by aineniamh
  0

• Not urgent - error running wg pipeline

  #238 opened 5 months ago by CatherineTroman
  5

• Similar database sequences leading to ambiguous mappings

  #219 opened 5 months ago by AShaw1802
  3

• Error running wg analysis mode: cannot find WG snakefile (piranha_wg.smk)

  #239 opened 5 months ago by eduardoscopel
  2

• Error when running piranha cl and gui

  #240 opened 5 months ago by cathrnbp
  2

• New install issue - Snakemake and PuLP conflict

  #234 opened 8 months ago by Desperate-Dan
  1

• Error when running haplotyping

  #230 opened 9 months ago by CatherineTroman
  2

• Rapid barcoding kit

  #225 opened 9 months ago by a-qvecell
  2

• ERROR: Failed building wheel for medaka

  #223 opened 9 months ago by a-qvecell
  7

• Labels not visible on tree in report

  #226 opened 9 months ago by AShaw1802
  2

• Lack of sequences from supplementary-datadir in trees generated by phylo module

  #224 opened 10 months ago by AShaw1802
  2

• Copy fastq data and barcodes CSV to output folder for storage and archiving

  #215 opened a year ago by rambaut
  1

• make category to bin by configurable- so by default ddns_group (previously display_name), but can change to species or whatever if doing EV sequencing

  #211 opened a year ago by aineniamh
  2

• barcode report header bug- all same

  #213 opened a year ago by aineniamh
  1

• fix the wpv variation plots in haplo dev so they're against cns rather than ref

  #214 opened a year ago by aineniamh
  1

• make display_name a more sensible category: change to ddns_group

  #210 opened a year ago by aineniamh
  1

• min percentage not met- still make a consensus sequence

  #208 opened a year ago by aineniamh
  1

• smaller percentage allowable if meets read threshold

  #209 opened a year ago by aineniamh
  0

• position rather than genome position in snipit x axis label

  #202 opened a year ago by aineniamh
  2

• barcode to show in the id seqs table

  #201 opened a year ago by aineniamh
  1

• new table with reads mapped/ found across all samples

  #199 opened a year ago by aineniamh
  1

• table only dynamically sho columns if there are any reads across samples for that ref group col

  #200 opened a year ago by aineniamh
  1

• Dont put date in supp datadir additions- just runname.fasta and runname.csv, runname may be dated

  #204 opened a year ago by aineniamh
  1

• if background is going to get very big with auto-accumulation, think of a way to boil it down to a smaller sample.

  #207 opened a year ago by aineniamh
  0

• show header fields from seqs in background and newly generated in metadata

  #206 opened a year ago by aineniamh
  0

• in phylo plot, strip empty fields

  #205 opened a year ago by aineniamh
  0

• runname in phylo tips

  #203 opened a year ago by aineniamh
  0