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Update documentation #136

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lucventurini opened this issue Oct 16, 2018 · 5 comments · Fixed by #400
Closed

Update documentation #136

lucventurini opened this issue Oct 16, 2018 · 5 comments · Fixed by #400
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@lucventurini
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@lucventurini
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The documentation for Mikado might need some refreshing in some areas, to clarify points and update on the latest developments. This should be completed before we release the next version.
@lucventurini lucventurini added this to the 1.3 milestone Oct 16, 2018
lucventurini added a commit that referenced this issue Oct 16, 2018
@lucventurini
Starting to work on #136. Also, updated the pick command line to allo…
1f19c18 
…w setting padding parameters.
@lucventurini lucventurini self-assigned this Oct 16, 2018
lucventurini added a commit that referenced this issue Oct 26, 2018
@lucventurini
Updated command lines for the three main programs in the documentation (
e43cb79 
#136)
lucventurini added a commit that referenced this issue Apr 2, 2019
@lucventurini
Minor edit to the docs (#136)
3f521e1
lucventurini added a commit to lucventurini/mikado that referenced this issue Aug 2, 2019
@lucventurini
Modified the CHANGELOG.md, starting to work properly on EI-CoreBioinf…
33e75bd 
…ormatics#136
lucventurini added a commit to lucventurini/mikado that referenced this issue Aug 5, 2019
@lucventurini
Starting correcting the docs for EI-CoreBioinformatics#136
c52c4c6
@lucventurini
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It is essential to make sure that the documentation explicitly explains that Mikado serialise must use ORFs called on the Mikado prepare output, not on the input transcript assemblies. Otherwise fatal mistakes can happen, see #206.

This was referenced Oct 10, 2019
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lucventurini added a commit that referenced this issue Nov 19, 2019
@lucventurini
Close #239 (#249)
0723988 
Close #239. TOML is fully supported, and allows to create far clearer configuration files.
Contestually, fixed a lot of the documentation for the configuration files (#136).
lucventurini added a commit to lucventurini/mikado that referenced this issue Nov 27, 2019
@lucventurini
EI-CoreBioinformatics#136: now "simple" configuration files are actua…
8d5cb1c 
…lly *simple*. Modifications related to this.
lucventurini added a commit to lucventurini/mikado that referenced this issue Nov 27, 2019
@lucventurini
EI-CoreBioinformatics#136: fixed the tests
f871716
@lucventurini
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Hi @ljyanesm , I have updated the documentation and the comments for the configuration files in the issue-136 branch.

This branch is strictly for modifying the documentation, comments of the configuration files and, at most, solving bugs related to either of the conditions above (hence my faffing around with the configuration this morning - however, the modifications do not modify the running of Mikado per se).

lucventurini added a commit to lucventurini/mikado that referenced this issue Nov 27, 2019
@lucventurini
EI-CoreBioinformatics#136: solved another small bug in the tests
f7c3789
@ljyanesm
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Hi @lucventurini, I can't see the branch you mention. Could it be in a different fork of this project?

@lucventurini
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Hi @ljyanesm,
you are right, it's on my personal fork. I just pushed it here as well.

@lucventurini lucventurini added this to High priority in Version 2 Oct 15, 2020
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Update: with 2f5a6b8, the issue-136 branch is now current with all the rest of the modifications.

@swarbred , as discussed by chat, on this branch I have also introduced the ability of specifiying per-sample stripping of the CDS during prepare and per-sample protection from the chimera splitting.

I have revised the documentation for the configuration and the algorithms, working my way through the other stages of the pipeline.

@lucventurini lucventurini mentioned this issue Dec 2, 2020
Merged
@lucventurini lucventurini removed this from High priority in Version 2 Jan 28, 2021
@lucventurini lucventurini removed this from the 2.0 milestone Jan 28, 2021
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Starting to work on EI-CoreBioinformatics#136. Also, updated the pick…
7b5d945 
… command line to allow setting padding parameters.
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Updated command lines for the three main programs in the documentation (
959a9e9 
EI-CoreBioinformatics#136)
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
First fix for EI-CoreBioinformatics#141: now transcripts are selected…
eea5825 
… on the basis of their source score. Properly tested, as per EI-CoreBioinformatics#137, and documentation updated, as per EI-CoreBioinformatics#136.
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
This commit should fix all the points regarding prepare for EI-CoreBi…
a15a3fb 
…oinformatics#141 and tests them properly (EI-CoreBioinformatics#137). We should still create tests for the mikado configure step, and update the documentation (EI-CoreBioinformatics#136).
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Updated documentation (EI-CoreBioinformatics#136), tests (EI-CoreBioi…
eacd917 
…nformatics#137) - including the daijin test, solved some minor bugs present in earlier commits, indicated the EICore repo as the main in the docs, now EI-CoreBioinformatics#141 should be ready to be closed
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Solved (hopefully) EI-CoreBioinformatics#142, updated the documentati…
a774758 
…on (EI-CoreBioinformatics#136)
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Updated documentation (EI-CoreBioinformatics#136)
9255a5e
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Minor edit to the docs (EI-CoreBioinformatics#136)
1827fb1
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Close EI-CoreBioinformatics#239 (EI-CoreBioinformatics#249)
73782e1 
Close EI-CoreBioinformatics#239. TOML is fully supported, and allows to create far clearer configuration files.
Contestually, fixed a lot of the documentation for the configuration files (EI-CoreBioinformatics#136).
lucventurini added a commit that referenced this issue Apr 1, 2021
@lucventurini
Merge branches 'documentation-update', 'expand_attributes_uses', 'iss…
3aa57e1 
…ue-395-pick-pad-crash' and 'issue-389-prepare-bed12-output' into version-2.2.4.

Fix #136 #395 #389 #397 #396 #385
@lucventurini lucventurini mentioned this issue Apr 1, 2021
Merged
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Version 2.2.4 EI-CoreBioinformatics/mikado
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@ljyanesm @lucventurini