bactopia/bactopia

Issues

• [question] Assembly Spades

  #513 opened a month ago by ingridvanw
  3

• WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested

  #515 opened a month ago by happymanmohit
  4

• Datasets [question]

  #511 opened a month ago by ingridvanw
  5

• BACTOPIA:GATHER:GATHER_MODULE (SRR2838702)'

  #512 opened a month ago by happymanmohit
  18

• [feature] BACTOPIATOOLS:MLST:MLST_MODULE untar database once in cache instead of for every sample

  #514 opened a month ago by nickjhathaway
  12

• Summary can't find the samples

  #509 opened 2 months ago by andreaniml
  31

• [bug] RuntimeError from Gubbins via Singularity in Snippy subworkflow

  #500 opened 2 months ago by pcrxn
  4

• [bug]Process `BACTOPIA:ASSEMBLER:ASSEMBLER_MODULE (reads)` terminated with an error exit status (1)

  #496 opened 3 months ago by happymanmohit
  33

• One file from Gubbins output is missing

  #510 opened a month ago by andreaniml
  4

• [bug] bactopia tools depend on uninstallable bioperl-1.7.2

  #502 opened 2 months ago by pvanheus
  15

• [bug] PIRATE cannot run because of unexpected extension

  #507 opened 2 months ago by telatin
  3

• How to mix public and local files

  #508 opened 2 months ago by andreaniml
  7

• Module installation

  #505 opened 2 months ago by aida-god92
  4

• Use local downloaded models for medaka in dragonflye module [feature]

  #506 opened 2 months ago by jenmuell
  2

• Conda create not working for bactopia 3.0.0

  #493 opened 3 months ago by JLHalpin
  5

• pre-existing bakta_db?[question]

  #504 opened 2 months ago by incoherentian
  2

• Staphtyper module compilation error

  #503 opened 2 months ago by Kiratrea
  2

• [bug] Error when using --medaka_model r941_min_sup_g507

  #470 opened 2 months ago by llk578496
  3

• [feature] Full AMRFinderPlus search combining results to get maximum information

  #487 opened 4 months ago by llk578496
  2

• [bug] cleanyerreads workflow fails in bactopia 3.0.1

  #501 opened 2 months ago by pvanheus
  1

• Bactopia-tools eggnog - decorate_gff option

  #495 opened 3 months ago by steven-bioinfo
  2

• Params and schema don't match (R1, R2, r1, r1)[bug]

  #473 opened 5 months ago by iferres
  4

• error message when installing Bactopia on an HPC cluster

  #486 opened 2 months ago by fransamsing
  2

• Error linking to bactopia results for ariba tool[bug]

  #488 opened 2 months ago by aperreault
  5

• roary module in pangenome failed [bug]

  #489 opened 2 months ago by aperreault
  10

• Error executing process > 'BACTOPIATOOLS:PANGENOME:CLONALFRAMEML:IQTREE (start-tree) [bug]

  #491 opened 2 months ago by aperreault
  10

• wf snippy fail

  #465 opened 2 months ago by ju6lio
  17

• 2024 Bactopia Usage Survey

  #499 opened 2 months ago by rpetit3
  0

• issue when using docker image

  #463 opened 2 months ago by ybdong919
  3

• [bug] bactopia search key error: maybe a bug, maybe my own misunderstanding

  #467 opened 2 months ago by amyecampbell
  19

• Tbprofiler collate automatically

  #466 opened 2 months ago by Caitgwill
  2

• Error creating Conda environment

  #469 opened 2 months ago by crisp3342
  6

• [bug] bactopia tool phispy does not find samples

  #472 opened 2 months ago by lfenske-93
  12

• MOB-Suite recon [bug]

  #478 opened 2 months ago by kruem-ar
  7

• abritamr bugs correction [bug]

  #477 opened 2 months ago by mtruglio
  4

• ncbigenomedownload is not a known workflow

  #480 opened 2 months ago by ktmeaton
  3

• Error creating conda environment during test [bug] [mac]

  #484 opened 2 months ago by aperreault
  9

• Sample IDs vs Experiment accessions

  #485 opened 2 months ago by andreaniml
  3

• --reference file not working for snippy tool [bug]

  #490 opened 2 months ago by aperreault
  4

• [bug] Poor quality / unmappeable samples cause `snippy-core` to fail with a confusing erorr message

  #494 opened 3 months ago by pvanheus
  0

• [bug] (or user error) kraken2 db not found

  #492 opened 3 months ago by incoherentian
  1

• [bug] PlasmidFinder CSV Concat doesn't include sample name column

  #481 opened 3 months ago by rwilliams
  4

• [feature] improve docs - add required parameters to doc site

  #483 opened 4 months ago by rpetit3
  0

• [feature] it should be easier to extract gene/protein alignments

  #482 opened 4 months ago by rpetit3
  1

• Include assembly genome in the pipeline

  #471 opened 4 months ago by felipe-mansoldo
  6

• [feature request] - add assembly accession support to bactopia search

  #476 opened 4 months ago by tfischer78
  6

• Run aborted,

  #475 opened 4 months ago by andreaniml
  6

• [question] Failed to install bactopia - didn't find info-linux-ppc64le_perl-5.32.1-4_ha17a0cc_perl5 component in /.../pkgs/linux-ppc64le_perl-5.32.1-4_ha17a0cc_perl5.conda

  #468 opened 4 months ago by siupenyau
  1

• [question] mapping directory

  #464 opened 7 months ago by Svnipni
  7

• [feature] [question] arcca_hawk.config

  #462 opened 7 months ago by incoherentian
  3