Skip to content

Latest commit

 

History

History
84 lines (70 loc) · 2.65 KB

CHANGELOG.md

File metadata and controls

84 lines (70 loc) · 2.65 KB
Raw

version 1.10.0

  • Fix crashing baseline when only unproductive sequences are present.
  • Replace "fast" option with options to toggle baseline and Change-O indidually.

version 1.9.1

  • Fix error in launch command.

version 1.9.0

  • Add a no filter region filter.
  • Fix a bug where tar would not open certain filenames.

version 1.8.1

  • Fix a bug where input files with spaces could not be used.
  • Fix a bug were the data format was not properly set for filtered IMGT archives.

version 1.8.0

  • Add options "Everything is IGA" and "Everything is IGG".
  • Make sure IGM naive and naive memory are part of the galaxy output.

version 1.7.0

  • Use the name of the input file to generate the name of the output IMGT archives.
  • Add same duplicate filters as immune repertoire pipeline.
  • Add a new "Everything is IGM" class filter for captured IGM sequences.
  • Fix bug where empty tables would cause crashes when generating plots.
  • Fix bug where R script errors where not written to stderr, causing galaxy to mistake the jobs as being successful.

version 1.6.0

  • Faster runtime due to faster gene identification, sequence overview creation and IMGT TAR archive creation.
  • Two extra IMGT files are provided. One for IGM with less than 2% mutations (naive) and one for IGM with more than 2% mutations (naive memory).
  • All IMGT files per sequence class are always provided regardless of how the Fast option is set. Previously this had to be set to no.
  • Fix a bug in sequence overview where links to unmatched sequences where not working properly in the by_id.html file.

version 1.5.0

  • Add an option to download all output files in a zip file.

version 1.4.0

  • Fix a bug where synonymous mutations where incorrectly parsed.
  • Use a container from biocontainers.

version 1.3.3

  • Fix a bug where tandem lengths were incorrectly calculated.

version 1.3.2

  • Fix a bug where the file removal process caused errors.

version 1.3.1

  • Fix issues with container discovery

version 1.3.0

  • Add missing dependencies to the requirements section.

version 1.2.0

  • Add a container in which the tool can execute.
  • Remove redundant files after execution.

version 1.1.0

  • Added changeo as a dependency. Porting to python3 was necessary to achieve this. This will make sure the shm_csr package can be installed on all galaxies.
  • Make sure the wrapper script runs with set -e -o pipefail and fails on error.
  • Updated all python scripts to work on python3