Mercurial > repos > davidvanzessen > shm_csr

annotate CHANGELOG.md @ 95:d63eff357515 draft

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planemo upload commit d96a736dcd6da34137f79861fbc6369716c332f1
author rhpvorderman
date Mon, 27 Mar 2023 13:11:53 +0000
parents 84e9e5c8c101
children 385dea3c6cb5
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1 version 1.8.1
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2 -----------------
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3 + Fix a bug where input files with spaces could not be used.
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4 + Fix a bug were the data format was not properly set for filtered IMGT
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5 archives.
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6
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7 version 1.8.0
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8 -----------------
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9 + Add options "Everything is IGA" and "Everything is IGG".
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10 + Make sure IGM naive and naive memory are part of the galaxy output.
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11
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12 version 1.7.0
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13 -----------------
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14 + Use the name of the input file to generate the name of the output IMGT
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15 archives.
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16 + Add same duplicate filters as immune repertoire pipeline.
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17 + Add a new "Everything is IGM" class filter for captured IGM sequences.
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18 + Fix bug where empty tables would cause crashes when generating plots.
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19 + Fix bug where R script errors where not written to stderr, causing galaxy to
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20 mistake the jobs as being successful.
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21
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22 version 1.6.0
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23 -------------
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24 + Faster runtime due to faster gene identification, sequence overview creation
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25 and IMGT TAR archive creation.
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26 + Two extra IMGT files are provided. One for IGM with less than 2% mutations
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27 (naive) and one for IGM with more than 2% mutations (naive memory).
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28 + All IMGT files per sequence class are always provided regardless of how the
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29 ``Fast`` option is set. Previously this had to be set to ``no``.
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30 + Fix a bug in sequence overview where links to unmatched sequences where not
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31 working properly in the by_id.html file.
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32
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33 version 1.5.0
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34 -------------
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35 + Add an option to download all output files in a zip file.
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36
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37 version 1.4.0
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38 -------------
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39 + Fix a bug where synonymous mutations where incorrectly parsed.
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40 + Use a container from biocontainers.
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41
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42 version 1.3.3
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43 -------------
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44 + Fix a bug where tandem lengths were incorrectly calculated.
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45
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46 version 1.3.2
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47 -------------
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48 + Fix a bug where the file removal process caused errors.
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49
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50 version 1.3.1
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51 -------------
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52 + Fix issues with container discovery
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53
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54 version 1.3.0
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55 -------------
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56 + Add missing dependencies to the requirements section.
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57
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58 version 1.2.0
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59 -------------
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60 + Add a container in which the tool can execute.
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61 + Remove redundant files after execution.
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62
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63 version 1.1.0
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64 -------------
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65 + Added changeo as a dependency. Porting to python3 was necessary to achieve
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66 this. This will make sure the shm_csr package can be installed on all
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67 galaxies.
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68 + Make sure the wrapper script runs with `set -e -o pipefail` and fails on
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69 error.
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70 + Updated all python scripts to work on python3