[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -1,18 +1,18 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
   - repo: https://github.com/snakemake/snakefmt
-    rev: v0.6.1
+    rev: v2.0.1
     hooks:
       - id: snakefmt
-  - repo: https://github.com/psf/black
-    rev: 22.6.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.5.1
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/isort.git
-    rev: 5.10.1
+    rev: 9.0.0a3
     hooks:
       - id: isort
   - repo: https://github.com/python-poetry/poetry

mccoy/workflow/Snakefile

@@ -4,7 +4,6 @@ import yaml
 import snakemake
 import pathlib
 
-
 PROJECT_DIR = Path(config['project_path'])
 RESOURCES_DIR = PROJECT_DIR / "resources"
 INPUT_DATA = config['data']
@@ -44,7 +43,6 @@ onstart:
     print("Workflow paths:")
     print(f"\t{'snakefile':20s} ➡  {workflow.snakefile}")
     print(f"\t{'working directory':20s} ➡  {workflow.basedir}")
-
     print("Environment:")
     shell = lambda cmd: subprocess.run(cmd, shell=True, stdout=subprocess.PIPE).stdout.decode().rstrip()
     print(f"\t{shell('python --version'):20s} ➡  {shell('which python')}")

mccoy/workflow/rules/align.smk

@@ -1,20 +1,20 @@
 rule align:
     """
-    Use `MAFFT <https://github.com/GSLBiotech/mafft>`_ to align the combined sequence file against the project
-    reference.
+Use `MAFFT <https://github.com/GSLBiotech/mafft>`_ to align the combined sequence file against the project
+reference.
 
-    :input original:   the combined sequence file generated from the :smk:ref:`combine` rule
-    :input reference:  the project reference sequence, provided during McCoy project creation
+:input original:   the combined sequence file generated from the :smk:ref:`combine` rule
+:input reference:  the project reference sequence, provided during McCoy project creation
 
-    :config align.mafft:      a list of command line arguments passed directly to MAFFT
-    :config align.threads:    the number of threads (cores) to use for a single MAFFT call
-    :config align.resources:  the resources to request when submitting to a cluster
+:config align.mafft:      a list of command line arguments passed directly to MAFFT
+:config align.threads:    the number of threads (cores) to use for a single MAFFT call
+:config align.resources:  the resources to request when submitting to a cluster
 
-    :output:     the aligned version of the original input file
-    :params:     the command-line arguments passed to MAFFT (set in `align.mafft` config entry)
-    :threads:    set to `align.threads` from the config file if present, else set by the number of cores available to the workflow (up-to `threads_max`)
-    :resources:  set to `align.resources` in the project config, if present
-    """
+:output:     the aligned version of the original input file
+:params:     the command-line arguments passed to MAFFT (set in `align.mafft` config entry)
+:threads:    set to `align.threads` from the config file if present, else set by the number of cores available to the workflow (up-to `threads_max`)
+:resources:  set to `align.resources` in the project config, if present
+"""
     input:
         original="data/combined/{id}.fasta",
         reference=RESOURCES_DIR / "reference.fasta",
@@ -24,25 +24,23 @@ rule align:
         "logs/align-{id}.txt",
     conda:
         "../envs/mafft.yml"
-    params:
-        lambda wildcards: " ".join(config["align"]["mafft"]),
     threads: config["align"].get("threads", config["all"]["threads_max"])
     resources:
         **config["align"].get("resources", {}),
+    params:
+        lambda wildcards: " ".join(config["align"]["mafft"]),
     shell:
         """
         REFNAME=$(head -n1 {input.reference} | tr -d '>')
-        mafft --thread {threads} {params} {input.original} {input.reference} 2> {log} \
-            | seqkit grep -rvip "^$REFNAME" > {output} 2> {log}
+        mafft --thread {threads} {params} {input.original} {input.reference} 2>{log} \
+            | seqkit grep -rvip "^$REFNAME" >{output} 2>{log}
         """
 
 
 rule alignment_stats:
     input:
         alignment=rules.align.output,
         reference=RESOURCES_DIR / "reference.fasta",
-    conda:
-        "../envs/steenwyk.yml"
     output:
         summary="results/aligned/{id}.summary.txt",
         gc_content="results/aligned/{id}.gc_content.txt",
@@ -51,13 +49,15 @@ rule alignment_stats:
         pairwise_identity_verbose="results/aligned/{id}.pairwise_identity_verbose.txt",
         # position_specific_score_matrix="results/aligned/{id}.position_specific_score_matrix.txt",
         # sum_of_pairs_score="results/aligned/{id}.sum_of_pairs_score.txt",
+    conda:
+        "../envs/steenwyk.yml"
     shell:
         """
-        biokit alignment_summary {input.alignment} > {output.summary}
-        phykit gc_content {input.alignment} > {output.gc_content}
-        phykit relative_composition_variability {input.alignment} > {output.relative_composition_variability}
-        phykit pairwise_identity {input.alignment} > {output.pairwise_identity}
-        phykit pairwise_identity {input.alignment} --verbose > {output.pairwise_identity_verbose}
+        biokit alignment_summary {input.alignment} >{output.summary}
+        phykit gc_content {input.alignment} >{output.gc_content}
+        phykit relative_composition_variability {input.alignment} >{output.relative_composition_variability}
+        phykit pairwise_identity {input.alignment} >{output.pairwise_identity}
+        phykit pairwise_identity {input.alignment} --verbose >{output.pairwise_identity_verbose}
 
         # phykit sum_of_pairs_score {input.alignment} --reference {input.reference} > output.sum_of_pairs_score
         # biokit position_specific_score_matrix {input.alignment}  > output.position_specific_score_matrix
@@ -67,11 +67,11 @@ rule alignment_stats:
 rule pairwise_identity_histogram:
     input:
         rules.alignment_stats.output.pairwise_identity_verbose,
-    conda:
-        "../envs/plot_traces.yml"
     output:
         svg="results/aligned/{id}.pairwise_identity_verbose.svg",
         html="results/aligned/{id}.pairwise_identity_verbose.html",
+    conda:
+        "../envs/plot_traces.yml"
     shell:
         """
         ${{CONDA_PREFIX}}/bin/python {SCRIPT_DIR}/pairwise_identity_histogram.py {input} {output.svg} {output.html}

mccoy/workflow/rules/beast.smk

@@ -1,22 +1,22 @@
 rule onlinebeast:
     """
-    Use `online-beast <https://github.com/Wytamma/online-beast>`_ to add any new
-    sequences to the Beast2 analysis from an inherited run and update the state.
+Use `online-beast <https://github.com/Wytamma/online-beast>`_ to add any new
+sequences to the Beast2 analysis from an inherited run and update the state.
 
-    .. warning::
-        This rule will only run if the ``--inherit`` or ``--inherit-last`` flags are passed to McCoy.
+.. warning::
+    This rule will only run if the ``--inherit`` or ``--inherit-last`` flags are passed to McCoy.
 
 
-    :input xml:        the template file generated by the :smk:ref:`dynamicbeast` rule
-    :input state:      the statefile from the inherited McCoy run.
-                       This is compied into the ``data`` directory by the McCoy CLI.
-    :input alignment:  the aligned sequences from the :smk:ref:`align` rule
+:input xml:        the template file generated by the :smk:ref:`dynamicbeast` rule
+:input state:      the statefile from the inherited McCoy run.
+                   This is compied into the ``data`` directory by the McCoy CLI.
+:input alignment:  the aligned sequences from the :smk:ref:`align` rule
 
-    :output:           the updated state file produced by online-beast.
+:output:           the updated state file produced by online-beast.
 
-                       **Note:** No XML file is produced as we are using a template XML which
-                       doesn't actually contain the sequences in it.
-    """
+                   **Note:** No XML file is produced as we are using a template XML which
+                   doesn't actually contain the sequences in it.
+"""
     input:
         xml=rules.dynamicbeast.output,
         state="data/{id}-beast.xml.state",
@@ -44,34 +44,35 @@ def beast_params(wildcards):
 
 rule beast:
     """
-    Run Beast2, either restarting from a state file or from scratch.
+Run Beast2, either restarting from a state file or from scratch.
 
-    .. note::
-        GPU acceleration is requested if available by default. If you are running on a machine with a compatible GPU then
-        the code will crash when using the bioconda package. To avoid this, either:
+.. note::
+    GPU acceleration is requested if available by default. If you are running on a machine with a compatible GPU then
+    the code will crash when using the bioconda package. To avoid this, either:
 
-        1. ensure you pass ``--use-envmodules`` to McCoy and set the ``envmodules`` directives of this rule appropriately, or
-        2. remove the ``-beagle_GPU`` flag from the  ``beast.beast`` entry in your McCoy config file. 
+    1. ensure you pass ``--use-envmodules`` to McCoy and set the ``envmodules`` directives of this rule appropriately, or
+    2. remove the ``-beagle_GPU`` flag from the  ``beast.beast`` entry in your McCoy config file.
 
-    :input alignment:         the aligned fasta file output from :smk:ref:`align`
-    :input template:          the Beast 2 input XML file, templated with `feast <https://github.com/tgvaughan/feast>`_.
-                              If ``inherit`` is set in the config then the output of the :smk:ref:`onlinebeast` rule is used,
-                              otherwise the output of the :smk:ref:`dynamicbeast` rule is used.
+:input alignment:         the aligned fasta file output from :smk:ref:`align`
+:input template:          the Beast 2 input XML file, templated with `feast <https://github.com/tgvaughan/feast>`_.
+                          If ``inherit`` is set in the config then the output of the :smk:ref:`onlinebeast` rule is used,
+                          otherwise the output of the :smk:ref:`dynamicbeast` rule is used.
 
-    :output:                  the tree log, trace log, and statefile from Beast2
+:output:                  the tree log, trace log, and statefile from Beast2
 
-    :config inherit:          are we inheriting from a previous run?
-    :config beast.dynamic:    the dynamic variables used to populate the feast template.
-    :config beast.beast:      Beast2 command line arguments to pass (beyond the params, statefile and input)
-    :config beast.threads:    the number of cores to run with (both locally or when submitting to a cluster)
-    :config beast.resources:  the resources to request when submitting to a cluster
+:config inherit:          are we inheriting from a previous run?
+:config beast.dynamic:    the dynamic variables used to populate the feast template.
+:config beast.beast:      Beast2 command line arguments to pass (beyond the params, statefile and input)
+:config beast.threads:    the number of cores to run with (both locally or when submitting to a cluster)
+:config beast.resources:  the resources to request when submitting to a cluster
 
-    :envmodules:              environment variables to load for the Spartan HPC system
+:envmodules:              environment variables to load for the Spartan HPC system
 
-    ..note::
-        GPU acceleration is **not** requested by default. If you are running on a machine with a compatible GPU then
-        please replace ``-beagle`` with ``-beagle_GPU`` in the ``beast.beast`` entry in your McCoy ``config.yaml`` file.
-    """
+..note::
+    GPU acceleration is **not** requested by default. If you are running on a machine with a compatible GPU then
+    please replace ``-beagle`` with ``-beagle_GPU`` in the ``beast.beast`` entry in your McCoy ``config.yaml`` file.
+
+"""
     input:
         alignment=rules.align.output,
         template=rules.dynamicbeast.output,
@@ -84,25 +85,25 @@ rule beast:
         "logs/{id}_beast.log",
     conda:
         "../envs/beast.yml"
-    params:
-        dynamic=lambda wildcards: ",".join(config["beast"]["dynamic"]),
-        beast=beast_params,
+    envmodules:
+        *config["beast"].get("envmodules", []),
     threads: config["beast"].get("threads", config["all"]["threads_max"])
     resources:
         **config["beast"].get("resources", {}),
-    envmodules:
-        *config["beast"].get("envmodules", []),
+    params:
+        dynamic=lambda wildcards: ",".join(config["beast"]["dynamic"]),
+        beast=beast_params,
     shell:
         """
         if [[ -n "{input.statefile}" ]]; then cp {input.statefile} {output.statefile}; fi
-        beast -D 'alignment={input.alignment},tracelog={output.tracelog},treelog={output.treelog},mcmc.threads={threads},{params.dynamic}' {params.beast} -statefile {output.statefile} {input.template} 1>&2 2> {log}
+        beast -D 'alignment={input.alignment},tracelog={output.tracelog},treelog={output.treelog},mcmc.threads={threads},{params.dynamic}' {params.beast} -statefile {output.statefile} {input.template} 1>&2 2>{log}
         """
 
 
 rule plot_traces:
     """
-    Makes trace plots from the beast log file.
-    """
+Makes trace plots from the beast log file.
+"""
     input:
         expand(rules.beast.output.tracelog, id=config['id']),
     output:
@@ -117,8 +118,8 @@ rule plot_traces:
 
 rule arviz:
     """
-    Makes trace plots from the beast log file.
-    """
+Makes trace plots from the beast log file.
+"""
     input:
         expand(rules.beast.output.tracelog, id=config['id']),
     output:
@@ -135,8 +136,8 @@ rule arviz:
 
 rule max_clade_credibility_tree:
     """
-    Makes trace plots from the beast log file.
-    """
+Makes trace plots from the beast log file.
+"""
     input:
         expand(rules.beast.output.treelog, id=config['id']),
     output:
@@ -151,8 +152,8 @@ rule max_clade_credibility_tree:
 
 rule max_clade_credibility_tree_newick:
     """
-    Makes trace plots from the beast log file.
-    """
+Makes trace plots from the beast log file.
+"""
     input:
         expand(rules.max_clade_credibility_tree.output, id=config['id']),
     output:
@@ -165,8 +166,8 @@ rule max_clade_credibility_tree_newick:
 
 rule max_clade_credibility_tree_render:
     """
-    Renders the consensus maximum likelihood tree from iqtree in SVG and HTML format.
-    """
+Renders the consensus maximum likelihood tree from iqtree in SVG and HTML format.
+"""
     input:
         expand(rules.max_clade_credibility_tree_newick.output, id=config['id']),
     output:

mccoy/workflow/rules/combine.smk

@@ -1,10 +1,10 @@
 rule combine:
     """
-    Combine multiple sequence files together into a single file.
+Combine multiple sequence files together into a single file.
 
-    :input data: the sequence files to be concatenated 
-    :output:     a single concatenated fasta file
-    """
+:input data: the sequence files to be concatenated
+:output:     a single concatenated fasta file
+"""
     input:
         data=INPUT_DATA,
     output:
@@ -15,5 +15,5 @@ rule combine:
         "../envs/combine.yml"
     shell:
         """
-        cat {input.data} | sed s/\@/_/g | seqkit rmdup -n -o {output} 2> {log}
+        cat {input.data} | sed s/\@/_/g | seqkit rmdup -n -o {output} 2>{log}
         """

mccoy/workflow/rules/dynamicbeast.smk

@@ -1,16 +1,16 @@
 rule dynamicbeast:
     """
-    Use `dynamicbeast <https://github.com/Wytamma/dynamic-beast>`_ to generate
-    a dynamic BEAST2 XML template from a standard static one, for use with
-    `feast <https://github.com/tgvaughan/feast>`_.
+Use `dynamicbeast <https://github.com/Wytamma/dynamic-beast>`_ to generate
+a dynamic BEAST2 XML template from a standard static one, for use with
+`feast <https://github.com/tgvaughan/feast>`_.
 
-    :input template: the BEAST XML template file
-    :input phytest_report:  the phytest report file generated by the :smk:ref:`phytest` rule.
-                            By using this as an input, we ensure that this rule (and all downstream rules)
-                            only run when our quality control checks pass.
+:input template: the BEAST XML template file
+:input phytest_report:  the phytest report file generated by the :smk:ref:`phytest` rule.
+                        By using this as an input, we ensure that this rule (and all downstream rules)
+                        only run when our quality control checks pass.
 
-    :output:  the dynamic XML template file to be used by the :smk:ref:`onlinebeast` and/or :smk:ref:`beast` rules
-    """
+:output:  the dynamic XML template file to be used by the :smk:ref:`onlinebeast` and/or :smk:ref:`beast` rules
+"""
     input:
         template=RESOURCES_DIR / "template.xml",
         phytest_report="results/{id}-phytest.html",
@@ -22,5 +22,5 @@ rule dynamicbeast:
         "../envs/dynamicbeast.yml"
     shell:
         """
-        dynamic-beast {input.template} > {output} 2> {log}
+        dynamic-beast {input.template} >{output} 2>{log}
         """

mccoy/workflow/rules/phytest.smk

@@ -1,13 +1,13 @@
 rule phytest:
     """
-    Run quality control checks using `phytest <https://github.com/phytest-devs/phytest>`_.
+Run quality control checks using `phytest <https://github.com/phytest-devs/phytest>`_.
 
-    :input alignment:     the aligned fasta file from the :smk:ref:`align` rule
-    :input tree:          the maximum likelihood tree generated by the :smk:ref:`tree` rule
-    :input phytest_file:  the phytest test file
+:input alignment:     the aligned fasta file from the :smk:ref:`align` rule
+:input tree:          the maximum likelihood tree generated by the :smk:ref:`tree` rule
+:input phytest_file:  the phytest test file
 
-    :output:  The phytest html report, placed into the Snakemake report
-    """
+:output:  The phytest html report, placed into the Snakemake report
+"""
     input:
         alignment="results/aligned/{id}.fasta",
         tree="results/tree/{id}.fasta.treefile",
@@ -20,5 +20,5 @@ rule phytest:
         "../envs/phytest.yml"
     shell:
         """
-        phytest {input.phytest_file} -s {input.alignment} -t {input.tree} --report {output} -v > {log}
+        phytest {input.phytest_file} -s {input.alignment} -t {input.tree} --report {output} -v >{log}
         """