[med-svn] [Git][med-team/paleomix][upstream] New upstream version 1.3.5
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Oct 13 20:20:25 BST 2021
Étienne Mollier pushed to branch upstream at Debian Med / paleomix
Commits:
6a3334d7 by Étienne Mollier at 2021-10-13T21:16:21+02:00
New upstream version 1.3.5
- - - - -
8 changed files:
- CHANGES.md
- docs/conf.py
- docs/installation.rst
- paleomix/__init__.py
- paleomix/pipelines/bam/config.py
- paleomix/pipelines/bam/nodes.py
- paleomix/pipelines/bam/parts/prefix.py
- paleomix_environment.yaml
Changes:
=====================================
CHANGES.md
=====================================
@@ -1,5 +1,11 @@
# Changelog
+## [1.3.5] - 2021-10-12
+
+### Added
+ - Added command-line option to reduce/turn off validation with picard ValidateSamFile.
+
+
## [1.3.4] - 2021-09-23
### Added
@@ -752,8 +758,8 @@ the (partially) updated documentation now hosted on ReadTheDocs.
- Switching to more traditional version-number tracking.
-[Unreleased]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.4...HEAD
-[1.3.3]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.3...v1.3.4
+[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
[1.3.2]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.1...v1.3.2
[1.3.1]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.0...v1.3.1
=====================================
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 = "1.3.4"
+release = "1.3.5"
# -- 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==1.3.4
+ $ python3 -m pip install paleomix==1.3.5
To verify that the installation was carried out correctly, run the command `paleomix`::
$ paleomix
PALEOMIX - pipelines and tools for NGS data analyses
- Version: v1.3.4
+ Version: v1.3.5
...
@@ -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==v1.3.4
+ $ ./venv/bin/pip install paleomix==v1.3.5
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/v1.3.4/paleomix_environment.yaml > paleomix_environment.yaml
+ $ curl -fL https://github.com/MikkelSchubert/paleomix/releases/download/v1.3.5/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, 4)
+__version_info__ = (1, 3, 5)
__version__ = "%i.%i.%i" % __version_info__
=====================================
paleomix/pipelines/bam/config.py
=====================================
@@ -166,6 +166,18 @@ def add_run_command(subparsers):
"to the JRE (Jave Runtime Environment); e.g. to change the "
"maximum amount of memory (default is -Xmx4g)",
)
+ group.add_argument(
+ "--validation",
+ metavar="LEVEL",
+ type=str.lower,
+ choices=("off", "partial", "full"),
+ default="full",
+ help="Change the amount of validation performed using picard ValidateSamFile. "
+ "Set to 'full' to validate both intermediate and final BAM files; set to "
+ "'partial' to validate only the final BAM files; and set to 'off' to disable "
+ "validation. Reducing the amount of validation may greatly decrease the total "
+ "runtime",
+ )
# Removed options
parser.add_argument("--gatk-max-threads", help=SUPPRESS)
=====================================
paleomix/pipelines/bam/nodes.py
=====================================
@@ -24,7 +24,14 @@ from paleomix.nodes.picard import ValidateBAMNode
from paleomix.nodes.samtools import BAMIndexNode
-def index_and_validate_bam(config, prefix, node, log_file=None, create_index=True):
+def index_and_validate_bam(
+ config,
+ prefix,
+ node,
+ log_file=None,
+ create_index=True,
+ validation_levels=("full",),
+):
input_file, index_file = _get_input_files(node, prefix["IndexFormat"])
if not index_file and create_index:
node = BAMIndexNode(
@@ -32,6 +39,10 @@ def index_and_validate_bam(config, prefix, node, log_file=None, create_index=Tru
)
(index_file,) = node.output_files
+ # Only enable validation if the user picked a corresponding level
+ if config.validation not in validation_levels:
+ return node
+
ignored_checks = [
# Ignored since we may filter out misses and low-quality hits during
# mapping, which leads to a large proportion of missing PE mates..
=====================================
paleomix/pipelines/bam/parts/prefix.py
=====================================
@@ -24,8 +24,8 @@ import os
from paleomix.common.utilities import safe_coerce_to_tuple
from paleomix.nodes.picard import MergeSamFilesNode
-from paleomix.pipelines.bam.nodes import index_and_validate_bam
from paleomix.nodes.validation import DetectInputDuplicationNode
+from paleomix.pipelines.bam.nodes import index_and_validate_bam
class Prefix:
@@ -64,7 +64,11 @@ class Prefix:
dependencies=self.datadup_check,
)
validated_node = index_and_validate_bam(
- config=config, prefix=prefix, node=node, log_file=validated_filename
+ config=config,
+ prefix=prefix,
+ node=node,
+ log_file=validated_filename,
+ validation_levels=("full", "partial"),
)
return {output_filename: validated_node}
=====================================
paleomix_environment.yaml
=====================================
@@ -17,4 +17,4 @@ dependencies:
- r-gam
- r-inline
- pip:
- - paleomix==1.3.4
+ - paleomix==1.3.5
View it on GitLab: https://salsa.debian.org/med-team/paleomix/-/commit/6a3334d70c7ce4934c448dc02b3e3e9f353bc5d7
--
View it on GitLab: https://salsa.debian.org/med-team/paleomix/-/commit/6a3334d70c7ce4934c448dc02b3e3e9f353bc5d7
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