[med-svn] [Git][med-team/paleomix][upstream] New upstream version 1.3.7
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Aug 26 06:35:49 BST 2022
Andreas Tille pushed to branch upstream at Debian Med / paleomix
Commits:
34abe8a1 by Andreas Tille at 2022-08-26T07:33:12+02:00
New upstream version 1.3.7
- - - - -
12 changed files:
- CHANGES.md
- docs/installation.rst
- paleomix/__init__.py
- paleomix/common/argparse.py
- paleomix/nodegraph.py
- paleomix/nodes/commands.py
- paleomix/pipeline.py
- paleomix/pipelines/bam/mkfile.py
- paleomix/pipelines/bam/parts/lane.py
- paleomix/pipelines/bam/parts/summary.py
- paleomix/pipelines/bam/pipeline.py
- paleomix_environment.yaml
Changes:
=====================================
CHANGES.md
=====================================
@@ -1,5 +1,23 @@
# Changelog
+## [1.3.7] - 2022-08-22
+
+#### Added
+ - Added example to BAM pipeline YAML template, showing how to increase the maximum
+ allowed Phred score for AdapterRemoval. This is needed due to the value being
+ capped at 41 by default, lower than the maximum observed in some modern data.
+
+#### Fixed
+ - Fixed regression in config file parsing, that would cause failure if no value
+ was specified for an option.
+ - Fixed error message not being printed correctly when attempting to use Phred+64
+ data with BWA mem/bwasw.
+ - Fixed regressions that prevented the use of "regions of interest" in the BAM
+ pipeline.
+ - Fixed failure when using `--list-output-files` and auxilary files were missing
+ or dependecies were unmet. Output files are now printed.
+
+
## [1.3.6] - 2021-11-28
### Added
@@ -768,6 +786,7 @@ the (partially) updated documentation now hosted on ReadTheDocs.
- Switching to more traditional version-number tracking.
+[1.3.7]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.6...v1.3.7
[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
=====================================
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==1.3.6
+ $ python3 -m pip install paleomix==1.3.7
To verify that the installation was carried out correctly, run the command `paleomix`::
$ paleomix
PALEOMIX - pipelines and tools for NGS data analyses
- Version: v1.3.6
+ Version: v1.3.7
...
@@ -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==v1.3.6
+ $ ./venv/bin/pip install paleomix==v1.3.7
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/v1.3.6/paleomix_environment.yaml > paleomix_environment.yaml
+ $ curl -fL https://github.com/MikkelSchubert/paleomix/releases/download/v1.3.7/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, 6)
+__version_info__ = (1, 3, 7)
__version__ = "%i.%i.%i" % __version_info__
=====================================
paleomix/common/argparse.py
=====================================
@@ -58,7 +58,7 @@ class ArgumentParser(configargparse.ArgumentParser):
def convert_item_to_command_line_arg(self, action, key, value):
# Ignore empty options from old config files
- if action and value == "=":
+ if action and value in ("", "="):
return []
return super().convert_item_to_command_line_arg(action, key, value)
=====================================
paleomix/nodegraph.py
=====================================
@@ -103,7 +103,12 @@ class NodeGraph:
NUMBER_OF_STATES = 6
DONE, RUNNING, RUNABLE, QUEUED, OUTDATED, ERROR = range(NUMBER_OF_STATES)
- def __init__(self, nodes, cache_factory=FileStatusCache):
+ def __init__(
+ self,
+ nodes,
+ allow_missing_files=False,
+ cache_factory=FileStatusCache,
+ ):
self._cache_factory = cache_factory
self._states = {}
self._state_counts = [0] * self.NUMBER_OF_STATES
@@ -126,17 +131,19 @@ class NodeGraph:
self._logger.info("Checking for auxiliary files")
if not self._check_auxiliary_files(self._reverse_dependencies):
- raise NodeGraphError(
- "Please refer to the PALEOMIX installation instructions at "
- "https://paleomix.readthedocs.io/en/stable/"
- )
+ if not allow_missing_files:
+ raise NodeGraphError(
+ "Please refer to the PALEOMIX installation instructions at "
+ "https://paleomix.readthedocs.io/en/stable/"
+ )
self._logger.info("Checking required software")
if not self._check_version_requirements(self._reverse_dependencies):
- raise NodeGraphError(
- "Please refer to the PALEOMIX installation instructions at "
- "https://paleomix.readthedocs.io/en/stable/"
- )
+ if not allow_missing_files:
+ raise NodeGraphError(
+ "Please refer to the PALEOMIX installation instructions at "
+ "https://paleomix.readthedocs.io/en/stable/"
+ )
self._logger.info("Determining states")
self._refresh_states()
=====================================
paleomix/nodes/commands.py
=====================================
@@ -104,7 +104,8 @@ class DepthHistogramNode(CommandNode):
if regions_file:
builder.set_option("--regions-file", "%(IN_REGIONS)s")
builder.set_kwargs(
- IN_REGIONS=regions_file, TEMP_IN_INDEX=input_file + index_format
+ IN_REGIONS=regions_file,
+ IN_INDEX=input_file + index_format,
)
CommandNode.__init__(
=====================================
paleomix/pipeline.py
=====================================
@@ -218,7 +218,11 @@ class Pypeline:
def list_output_files(self):
cache = FileStatusCache()
- nodegraph = NodeGraph(self._nodes, lambda: cache)
+ nodegraph = NodeGraph(
+ self._nodes,
+ allow_missing_files=True,
+ cache_factory=lambda: cache,
+ )
output_files = {}
def collect_output_files(node):
=====================================
paleomix/pipelines/bam/mkfile.py
=====================================
@@ -53,6 +53,9 @@ Options:
--collapse: yes
--trimns: yes
--trimqualities: yes
+ # Increase the maximum Phred allowed for input FASTQs, as well as for merged bases
+ # when using --collapse (default = 41). This is needed for some modern FASTQs.
+# --qualitymax: 42
"""
_TEMPLATE_BAM_OPTIONS = """ # Settings for aligners supported by the pipeline
=====================================
paleomix/pipelines/bam/parts/lane.py
=====================================
@@ -209,7 +209,7 @@ class Lane:
raise MakefileError(
"Mapping with BWA using the %r algorithm currently does not support "
"QualityOffsets other than 33; please convert your FASTQ if you wish "
- "to proceed."
+ "to proceed." % (parameters["algorithm"],)
)
parameters = self._set_pe_input_files(parameters)
=====================================
paleomix/pipelines/bam/parts/summary.py
=====================================
@@ -112,8 +112,8 @@ class SummaryTableNode(Node):
self._write_areas_of_interest(table, rois)
table.write("#\n#\n")
- for roi in rois.values():
- genomes[roi["Label"]] = {"Size": roi["Size"]}
+ for key, roi in rois.items():
+ genomes[":".join(key)] = {"Size": roi["Size"]}
self._write_tables(table, genomes)
def _teardown(self, _config, temp):
=====================================
paleomix/pipelines/bam/pipeline.py
=====================================
@@ -31,6 +31,7 @@ import paleomix.resources
import paleomix.yaml
from paleomix.pipeline import Pypeline
+from paleomix.node import NodeError
from paleomix.nodes.samtools import FastaIndexNode
from paleomix.nodes.bwa import BWAIndexNode
from paleomix.nodes.bowtie2 import Bowtie2IndexNode
@@ -206,10 +207,9 @@ def run(config, pipeline_variant):
logger.info("Building BAM pipeline for %r", makefile["Filename"])
try:
nodes = pipeline_func(config, makefile)
- except paleomix.node.NodeError as error:
- logger.error(
- "Error while building pipeline for %r:\n%s", makefile["Filename"], error
- )
+ except (NodeError, MakefileError) as error:
+ logger.error("Error while building pipeline for %r", makefile["Filename"])
+ logger.error("%s", error)
return 1
pipeline.add_nodes(*nodes)
=====================================
paleomix_environment.yaml
=====================================
@@ -17,4 +17,4 @@ dependencies:
- r-gam
- r-inline
- pip:
- - paleomix==1.3.6
+ - paleomix==1.3.7
View it on GitLab: https://salsa.debian.org/med-team/paleomix/-/commit/34abe8a11ed0d190c24f6d649f69ae2d7c2d08fb
--
View it on GitLab: https://salsa.debian.org/med-team/paleomix/-/commit/34abe8a11ed0d190c24f6d649f69ae2d7c2d08fb
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