[med-svn] [Git][med-team/paleomix][upstream] New upstream version 1.3.6

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / paleomix


Commits:
4ecb3fd4 by Étienne Mollier at 2021-12-11T21:23:00+01:00
New upstream version 1.3.6
- - - - -


7 changed files:

- CHANGES.md
- docs/conf.py
- docs/installation.rst
- paleomix/__init__.py
- paleomix/nodes/adapterremoval.py
- paleomix/pipelines/bam/makefile.py
- paleomix_environment.yaml


Changes:

=====================================
CHANGES.md
=====================================
@@ -1,5 +1,15 @@
 # Changelog
 
+## [1.3.6] - 2021-11-28
+
+### Added
+  - Added explicit support for the AdapterRemoval `--trim5p` and `--trim3p` options,
+    which may take one or two values (as a list).
+
+### Changed
+  - User options for AdapterRemoval are no longer restricted by a whitelist.
+
+
 ## [1.3.5] - 2021-10-12
 
 ### Added
@@ -758,6 +768,7 @@ the (partially) updated documentation now hosted on ReadTheDocs.
   - Switching to more traditional version-number tracking.
 
 
+[1.3.6]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.5...v1.3.6
 [1.3.5]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.4...v1.3.5
 [1.3.4]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.3...v1.3.4
 [1.3.3]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.2...v1.3.3


=====================================
docs/conf.py
=====================================
@@ -26,7 +26,7 @@ author = "Mikkel Schubert"
 # The short X.Y version
 version = "1.3"
 # The full version, including alpha/beta/rc tags
-release = "1.3.5"
+release = "1.3.6"
 
 
 # -- General configuration ---------------------------------------------------


=====================================
docs/installation.rst
=====================================
@@ -17,13 +17,13 @@ In addition, some libraries used by PALEOMIX may require additional development
 
 Once all requirements have been installed, PALEOMIX may be installed using `pip`::
 
-    $ python3 -m pip install paleomix==1.3.5
+    $ python3 -m pip install paleomix==1.3.6
 
 To verify that the installation was carried out correctly, run the command `paleomix`::
 
     $ paleomix
     PALEOMIX - pipelines and tools for NGS data analyses
-    Version: v1.3.5
+    Version: v1.3.6
 
     ...
 
@@ -45,7 +45,7 @@ This installation method requires the `venv` module. On Debian based systems, th
 Once `venv` is installed, creation of a virtual environment and installation of PALEOMIX may be carried out as shown here::
 
     $ python3 -m venv venv
-    $ ./venv/bin/pip install paleomix==v1.3.5
+    $ ./venv/bin/pip install paleomix==v1.3.6
 
 Following successful completion of these commands, the `paleomix` executable will be accessible in the `./venv/bin/` folder. However, as this folder also contains a copy of Python itself, it is not recommended to add it to your `PATH`. Instead, simply link the `paleomix` executable to a folder in your `PATH`. This can be accomplished as follows::
 
@@ -78,7 +78,7 @@ To install `conda` and also set it up so it can use the `bioconda`_ bioinformati
 
 Next, run the following commands to download the conda environment template for this release of PALEOMIX and to create a new conda environment named `paleomix` using that template::
 
-    $ curl -fL https://github.com/MikkelSchubert/paleomix/releases/download/v1.3.5/paleomix_environment.yaml > paleomix_environment.yaml
+    $ curl -fL https://github.com/MikkelSchubert/paleomix/releases/download/v1.3.6/paleomix_environment.yaml > paleomix_environment.yaml
     $ conda env create -n paleomix -f paleomix_environment.yaml
 
 You can now activate the paleomix environment with::


=====================================
paleomix/__init__.py
=====================================
@@ -21,5 +21,5 @@
 # SOFTWARE.
 #
 
-__version_info__ = (1, 3, 5)
+__version_info__ = (1, 3, 6)
 __version__ = "%i.%i.%i" % __version_info__


=====================================
paleomix/nodes/adapterremoval.py
=====================================
@@ -142,4 +142,14 @@ def _get_common_parameters(options, threads=1):
         cmd.cmd.set_option("--adapter-list", "%(IN_ADAPTER_LIST)s")
         cmd.command.set_kwargs(IN_ADAPTER_LIST=adapter_list)
 
+    for key in ("--trim5p", "--trim3p"):
+        values = options.pop(key, None)
+        if values is not None:
+            cmd.add_value(key)
+            if isinstance(values, list):
+                for value in values:
+                    cmd.add_value(value)
+            else:
+                cmd.add_value(values)
+
     return cmd


=====================================
paleomix/pipelines/bam/makefile.py
=====================================
@@ -173,6 +173,9 @@ _VALIDATION_OPTIONS = {
         "--preserve5p": Or(IsNone, IsBoolean),
         "--collapse-deterministic": Or(IsNone, IsBoolean),
         "--collapse-conservatively": Or(IsNone, IsBoolean),
+        "--trim5p": Or(IsInt, IsListOf(IsInt)),
+        "--trim3p": Or(IsInt, IsListOf(IsInt)),
+        StringStartsWith("--"): Or(IsStr, IsInt, IsFloat, IsNone),
     },
     # Which aliger/mapper to use (BWA/Bowtie2)
     "Aligners": {


=====================================
paleomix_environment.yaml
=====================================
@@ -17,4 +17,4 @@ dependencies:
   - r-gam
   - r-inline
   - pip:
-    - paleomix==1.3.5
+    - paleomix==1.3.6



View it on GitLab: https://salsa.debian.org/med-team/paleomix/-/commit/4ecb3fd49faf45b0f56280eb42f5af47f1fdfc77

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