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planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
author rhpvorderman
date Wed, 10 Jan 2024 12:32:47 +0000
parents fbc6307dd83b
children
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98
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1 version 1.10.0
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2 ------------------
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3 + Fix crashing baseline when only unproductive sequences are present.
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4 + Replace "fast" option with options to toggle baseline and Change-O indidually.
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5
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6 version 1.9.1
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7 -----------------
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8 + Fix error in launch command.
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9
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10 version 1.9.0
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11 -----------------
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12 + Add a no filter region filter.
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13 + Fix a bug where tar would not open certain filenames.
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14
95
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15 version 1.8.1
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16 -----------------
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17 + Fix a bug where input files with spaces could not be used.
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18 + Fix a bug were the data format was not properly set for filtered IMGT
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19 archives.
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20
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21 version 1.8.0
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22 -----------------
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23 + Add options "Everything is IGA" and "Everything is IGG".
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24 + Make sure IGM naive and naive memory are part of the galaxy output.
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25
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26 version 1.7.0
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27 -----------------
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28 + Use the name of the input file to generate the name of the output IMGT
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29 archives.
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30 + Add same duplicate filters as immune repertoire pipeline.
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31 + Add a new "Everything is IGM" class filter for captured IGM sequences.
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32 + Fix bug where empty tables would cause crashes when generating plots.
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33 + Fix bug where R script errors where not written to stderr, causing galaxy to
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34 mistake the jobs as being successful.
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35
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36 version 1.6.0
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37 -------------
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38 + Faster runtime due to faster gene identification, sequence overview creation
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39 and IMGT TAR archive creation.
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40 + Two extra IMGT files are provided. One for IGM with less than 2% mutations
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41 (naive) and one for IGM with more than 2% mutations (naive memory).
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42 + All IMGT files per sequence class are always provided regardless of how the
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43 ``Fast`` option is set. Previously this had to be set to ``no``.
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44 + Fix a bug in sequence overview where links to unmatched sequences where not
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45 working properly in the by_id.html file.
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46
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47 version 1.5.0
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48 -------------
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49 + Add an option to download all output files in a zip file.
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50
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51 version 1.4.0
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52 -------------
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53 + Fix a bug where synonymous mutations where incorrectly parsed.
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54 + Use a container from biocontainers.
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55
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56 version 1.3.3
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57 -------------
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58 + Fix a bug where tandem lengths were incorrectly calculated.
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59
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60 version 1.3.2
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61 -------------
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62 + Fix a bug where the file removal process caused errors.
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63
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64 version 1.3.1
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65 -------------
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66 + Fix issues with container discovery
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67
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68 version 1.3.0
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69 -------------
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70 + Add missing dependencies to the requirements section.
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71
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72 version 1.2.0
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73 -------------
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74 + Add a container in which the tool can execute.
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75 + Remove redundant files after execution.
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76
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77 version 1.1.0
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78 -------------
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79 + Added changeo as a dependency. Porting to python3 was necessary to achieve
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80 this. This will make sure the shm_csr package can be installed on all
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81 galaxies.
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82 + Make sure the wrapper script runs with `set -e -o pipefail` and fails on
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83 error.
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84 + Updated all python scripts to work on python3