Mercurial > repos > davidvanzessen > shm_csr

annotate CHANGELOG.md @ 94:84e9e5c8c101 draft

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"planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
author rhpvorderman
date Fri, 24 Mar 2023 16:58:28 +0000
parents 8fcf31272f6e
children d63eff357515
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1 version 1.8.0
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2 -----------------
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3 + Add options "Everything is IGA" and "Everything is IGG".
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
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4 + Make sure IGM naive and naive memory are part of the galaxy output.
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5
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6 version 1.7.0
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7 -----------------
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8 + Use the name of the input file to generate the name of the output IMGT
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9 archives.
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10 + Add same duplicate filters as immune repertoire pipeline.
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11 + Add a new "Everything is IGM" class filter for captured IGM sequences.
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12 + Fix bug where empty tables would cause crashes when generating plots.
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13 + Fix bug where R script errors where not written to stderr, causing galaxy to
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14 mistake the jobs as being successful.
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15
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16 version 1.6.0
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17 -------------
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18 + Faster runtime due to faster gene identification, sequence overview creation
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19 and IMGT TAR archive creation.
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20 + Two extra IMGT files are provided. One for IGM with less than 2% mutations
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21 (naive) and one for IGM with more than 2% mutations (naive memory).
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22 + All IMGT files per sequence class are always provided regardless of how the
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23 ``Fast`` option is set. Previously this had to be set to ``no``.
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24 + Fix a bug in sequence overview where links to unmatched sequences where not
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25 working properly in the by_id.html file.
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26
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27 version 1.5.0
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28 -------------
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29 + Add an option to download all output files in a zip file.
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30
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31 version 1.4.0
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32 -------------
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33 + Fix a bug where synonymous mutations where incorrectly parsed.
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34 + Use a container from biocontainers.
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35
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36 version 1.3.3
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37 -------------
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38 + Fix a bug where tandem lengths were incorrectly calculated.
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39
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40 version 1.3.2
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41 -------------
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42 + Fix a bug where the file removal process caused errors.
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43
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
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44 version 1.3.1
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45 -------------
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
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46 + Fix issues with container discovery
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47
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48 version 1.3.0
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49 -------------
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50 + Add missing dependencies to the requirements section.
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51
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52 version 1.2.0
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53 -------------
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
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54 + Add a container in which the tool can execute.
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55 + Remove redundant files after execution.
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56
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57 version 1.1.0
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58 -------------
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59 + Added changeo as a dependency. Porting to python3 was necessary to achieve
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60 this. This will make sure the shm_csr package can be installed on all
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61 galaxies.
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62 + Make sure the wrapper script runs with `set -e -o pipefail` and fails on
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63 error.
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64 + Updated all python scripts to work on python3