Commit 26ee05b8 authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'master' into 'dev'

Master

See merge request !789
parents 88bfd8f8 6edd4e9f
Pipeline #166232 passed with stages
in 8 minutes and 26 seconds
......@@ -127,6 +127,7 @@ algo_valgrind_functional:
release_valgrind_functional:
<<: *valgrind_functional
allow_failure: true
only:
- /^feature-.*a.*\/release$/
......
## Preparation
## Before the release
### Documentation
* [ ] New features are described in `doc/vidjil-algo.md`
* [ ] Breaking changes (or needed) are understood
* [ ] Breaking changes (and needed configuration changes) are understood
On the `feature-a/release` branch, the last commit is the release commit updating the three following files:
* [ ] CHANGELOG
* [ ] `doc/vidjil-algo.md` with the proper release tag
* [ ] `algo/release` with the proper release tag
## Pipelines
### Pipelines
https://gitlab.inria.fr/vidjil/vidjil/pipelines/XXXXX
(if tests passed on different pipelines, indicate below the relevant pipelines)
Usual tests should pass, but also:
* [ ] prepare_release
......@@ -23,21 +26,20 @@ Benchmarks
* [ ] almost no change...
* [ ] ... or significant changes are understood
## Tag and push
## The release, publish, tag and push
* [ ] merge this MR to *master* and tag: `git tag release-20XX-XX`
* [ ] push: `git push origin master release-20XX-XX`
* [ ] mirror to GH: `git push github master release-20XX.XX`
* [ ] click `publish_release` (there may be changes to CD...)
* [ ] tag (`git tag release-20XX-XX; git push origin release-20XX-XX`)
* [ ] mirror to GH
After these steps, we merge back the release in `dev`:
* [ ] merge this MR to dev
## Deploy
## After the release: deploy
* [ ] doc
* [ ] `app` (vidjil-algo-next)
* [ ] `app` if needed, update server configs
* [ ] `app` notification to users
* [ ] `app` (vidjil-algo)
* [ ] `app` test on production (X5 and L4)
* [ ] `hds` queue for qualification ?
* [ ] twice a year, communicate to users
Sometimes, the deploy stages can occur several days after the release.
Open a new internal issue with the "Deploy" template.
/label ~cpp
......@@ -13,9 +13,8 @@ $ Segment two reads on IgVC/IgJC (second -g option)
1: IgVC .* -> .* 1
1: IgJC .* -> .* 1
!LAUNCH: cat out/isotypes.vidjil
!NO_LAUNCHER:
!LAUNCH: cat out/isotypes.vidjil
$ Both germlines are in .vidjil
1: /germline"
......
......@@ -9,8 +9,8 @@ $ Report two clones, even with --max-consensus 0
: ==> 2 clones
!LAUNCH: cat out/Stanford_S22.vidjil
!NO_LAUNCHER:
!LAUNCH: cat out/Stanford_S22.vidjil
$ Labels are in the .json output
1: "label": "lab1"
......
This changelog concerns vijil-algo, the algorithmic part (C++) of the Vidjil platform.
2020-08-XX The Vidjil Team
* Cleaned output, no .vdj.fa and seq/clone-*.fa by default, new options --out-vdjfa and --out-clone-files #4386 #4387
Pipelines should not rely on the format of the headers in the .vdj.fa file, but rather parse the .vidjil file #3795
* Extended test and support to g++ 10.1, while reworking the documentation on supported compilers !733
* Updated documentation
* Updated the functional test framework (tools/should.py) !669 !784, new and updated tests
2020-06-12 The Vidjil Team
* New report of 'start of V' and 'end of J' positions #2138, improving the productivity estimation #2142
This is based on a streamlined alignment for reverse sequences (core/segment.cpp) !706
......
......@@ -9,8 +9,8 @@ pathologies, and in leukemia, are used to quantify the minimal residual
disease during patient follow-up.
With adapted [library preparation and sequencing](locus.md),
high-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](https://omictools.com/rep-seq-category)
methods and software.
enables the deep sequencing of a lymphoid population with dedicated
sequencing methods and software, called either Rep-Seq or AIRR-Seq.
### Life scientist
- Tutorial "Mastering the Vidjil web application":
......
......@@ -2,9 +2,9 @@
[V(D)J recombinations](http://en.wikipedia.org/wiki/V\(D\)J_recombination) in lymphocytes are essential for immunological diversity.
They are also useful markers of pathologies, and in leukemia, are used to quantify the minimal residual disease during patient follow-up.
high-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](https://omictools.com/rep-seq-category)
methods and software.
High-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated
sequencing methods and software, called either Rep-Seq or AIRR-Seq.
# Library preparation and sequencing for human RepSeq studies
......
......@@ -5,8 +5,8 @@ Vidjil is an open-source platform for the analysis of high-throughput sequencing
They are also useful markers of pathologies, and in leukemia, are used to quantify the minimal residual disease during patient follow-up.
With adapted [library preparation and sequencing](http://www.vidjil.org/doc/locus),
high-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](https://omictools.com/rep-seq-category)
methods and software.
enables the deep sequencing of a lymphoid population with dedicated
sequencing methods and software, called either Rep-Seq or AIRR-Seq.
This is the help of the [Vidjil web application](http://app.vidjil.org/).
Further help can always be asked to <support@vidjil.org>. We can also arrange phone or video meeting.
......@@ -420,7 +420,7 @@ inside a clone can have different lengths or can be shifted,
especially in the case of overlapping paired-end sequencing. There can be also
some sequencing errors.
The `.vidjil` file has to give one consensus sequence per clone, and
Rep-Seq algorithms have to deal with great care to these difference in
RepSeq algorithms have to deal with great care to these difference in
order not to gather reads from different clones.
For **vidjil-algo**, it is required that the window centered on
......
# vidjil-algo 2020.06
# vidjil-algo 2020.08
**Command-line manual**
*The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Tatiana and Rayan)*
......@@ -28,8 +28,8 @@ leukemia, are used to quantify the minimal residual disease during
patient follow-up.
With adapted [library preparation and sequencing](http://www.vidjil.org/doc/locus),
high-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](https://omictools.com/rep-seq-category)
methods and software.
enables the deep sequencing of a lymphoid population with dedicated
sequencing methods and software, called either Rep-Seq or AIRR-Seq.
Vidjil-algo processes high-throughput sequencing data to extract V(D)J
junctions and gather them into clones. Vidjil-algo starts
......@@ -496,7 +496,7 @@ Even if it is advised to rather use the full information in the `.vijdil` file,
the `.vdj.fa` is a convenient way to have sequences of clones for further processing.
These sequences are at least the windows (and their count in the headers) or
the consensus sequences (`--max-consensus`) when they have been computed.
The [headers](#headers-in-vdj-fa-files-deprecated) are described below, but the format of the headers is deprecated
The [headers](#headers-in-the-vdjfa-files-deprecated) are described below, but the format of the headers is deprecated
and will not be enforced in future releases.
Some other informations such as the further clustering are not output in this file.
......
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