Mercurial > repos > davidvanzessen > shm_csr
annotate CHANGELOG.md @ 98:d714f5ea83d7 draft default tip
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
author | rhpvorderman |
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date | Wed, 10 Jan 2024 12:32:47 +0000 |
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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 |
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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 |