Mercurial > repos > davidvanzessen > shm_csr
view CHANGELOG.md @ 96:385dea3c6cb5 draft
planemo upload commit 423a48569c69301fdbf893ac3a649128404dfff5
author | rhpvorderman |
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date | Fri, 05 Jan 2024 08:53:22 +0000 |
parents | d63eff357515 |
children | fbc6307dd83b |
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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