NorwegianVeterinaryInstitute/ALPPACA

Issues

• Panaroo core gene alignment issue

  #120 opened 5 months ago
  6

• Create over-arching workflow to run several tracks at once

  #119 opened 8 months ago
  0

• fix input to parsnp

  #117 opened 7 months ago
  0

• Correct the Gubbins conda version

  #116 opened 7 months ago
  0

• bootstrap display on branches

  #115 opened 8 months ago
  2

• Add gff files as optional output in core gene track

  #113 opened 9 months ago
  0

• Update ParSNP to version 2.0.0

  #112 opened 9 months ago
  2

• automation clustering - level selection and CC/simi

  #111 opened a year ago
  0

• implement the new version of gubbins - that can be sed fixed

  #109 opened 10 months ago
  2

• identity thresholds in panaroo

  #108 opened 10 months ago
  0

• gene presence absence table

  #107 opened 10 months ago
  0

• Review output hamming distances

  #106 opened 10 months ago
  0

• Add monocytogenes scheme to MLST image - maybe

  #105 opened 10 months ago
  3

• Add Apptainer profile

  #103 opened 2 years ago
  0

• Check the new version of chewBBACA

  #102 opened 10 months ago
  0

• wiki - clarify - the mapping analysis example

  #101 opened 2 years ago
  1

• Add filtering check step for cgmlst track

  #94 opened 2 years ago
  3

• Normalize distance for cgMLST

  #93 opened 2 years ago
  2

• latest image chewbbaca

  #92 opened 2 years ago
  2

• snp-dists -m option please

  #91 opened 2 years ago
  3

• Add option for outputting unaligned regions

  #88 opened 2 years ago
  1

• Add option for quick phylogeny

  #86 opened 10 months ago
  1

• ALPPACA - FASTANI - wrap script : clean fastANI results + statistics + tree that can be viewed

  #78 opened 2 years ago
  3

• Add iqtree parameter seed

  #72 opened 2 years ago
  1

• sample sheet not checked for missing files

  #65 opened 2 years ago
  1

• Switch from Prokka to Bakta

  #54 opened 10 months ago
  8

• Create test workflows for core gene and mapping tracks

  #51 opened 2 years ago
  3

• Minor comment on the structure of the JOSS submission

  #45 opened 2 years ago
  7

• Add fastani - evaluation diversity - and clustering

  #43 opened 2 years ago
  6

• integrate cgMLST typing

  #42 opened 2 years ago
  6

• Quality of writing: The "Tracks" section reads more like a methodology section (we ran this, then that, then this) instead of specifying the unique properties of each pipeline, and some results of expected output on real datasets. The "Conclusion" section makes more or less the same statements as the Summary and do not provide any additional insights into the future of this research.

  #41 opened 2 years ago
  1

• State of the field: As far as I know, the authors do not include a state of the field.

  #40 opened 2 years ago
  1

• Statement of need This section seems to repeat many times that the authors implemented a pipeline for phylogenetic analysis of prokaryotic genomes. I'd be interested in learning about other works discussing the need for a solution to the problem the authors attempt to solve, or about the way in which the different tracks differ from each other.

  #39 opened 2 years ago
  1

• Summary: The summary consists of statements that are too generic (e.g. XXX is often a complex and time-consuming process) or that are very technical and not relevant at this stage of the manuscript (e.g. "The pipeline is implemented in Nextflow and utilize singularity containers, which makes the pipeline portable and reproducible.", "The final results are presented in a tidy HTML report for each track. The code, documentation and examples of configuration files to run analyses with are publicly available on Github.")The authors should provide a high level description of what problems they try to solve and how they did it.

  #38 opened 2 years ago
  0

• For Shell scripts in the main directory and in bin, please update the shebang lines to #!/usr/bin/env bash, which is more flexible for different environments your users may have.

  #37 opened 2 years ago
  0

• Community guidelines: No instructions for third parties wishing to contribute to the software found.

  #36 opened 2 years ago
  1

• Automated tests: There are no automated tests to verify the functionality of the software. I understand that the pipeline requires an HPC to run the full pipeline, but automated tests could be made possible by unit testing the individual modules and/or integration testing on a subset of the original data.

  #35 opened 2 years ago
  6

• Statement of need: The wiki does not list a statement of need

  #34 opened 2 years ago
  1

• The repository README should mention that the documentation is stored in the repository Wiki.

  #33 opened 2 years ago
  1

• Functionality > Installation: Simplify installation procedures in line with typical Nextflow pipelines

  #32 opened 2 years ago
  1

• add an env.yml

  #31 opened 2 years ago
  1

• restructure config files

  #30 opened 2 years ago
  1

• remove wrapper script for running the pipeline

  #29 opened 2 years ago
  1

• Fix dependency handling

  #28 opened 2 years ago
  3

• Comments on JOSS submission

  #27 opened 2 years ago
  8

• Recomb detection in core gene?

  #26 opened 2 years ago
  0

• SNP distance calculations

  #25 opened 2 years ago
  0

• Make proper test for pipeline

  #24 opened 2 years ago
  0

• MFP configfile fix

  #22 opened 3 years ago
  0

• wiki / general - improvement - questions

  #21 opened 2 years ago
  0