feat: wrapper for cnvkit batch (#1877)

### Description

Wrapper for cnvkit batch which supports calling and reference creation 

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] I confirm that:

For all wrappers added by this PR, 

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* temporary files are either written to a unique hidden folder in the
working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).

---------

Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>

bio/cnvkit/batch/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - cnvkit =0.9.10

bio/cnvkit/batch/meta.yaml

@@ -0,0 +1,23 @@
+name: cnvkit batch
+description: >
+  Run the CNVkit pipeline on one or more BAM files to call cnv alterations.
+  Or use it to generate a new reference file
+url: https://cnvkit.readthedocs.io/en/stable/pipeline.html
+authors:
+  - Patrik Smeds
+input:
+  - bam: one or more bam files
+  - reference: copy reference file, when calling samples
+  - fasta: reference gneome, when building new reference
+  - antitarget: bed antitarget file, when building new reference
+  - target: bed target file, when building new reference
+  - mappability: mappability file, when building new reference
+output:
+  - >
+    a set of cnvkit generated files, multiple types of cns, cnr and cnn files
+  - or a new reference file
+params:
+  method: >
+    Optional, if no value is set cnvkits default value will be use
+  extra: Any additional arguments to pass
+notes:

bio/cnvkit/batch/test/Snakefile

@@ -0,0 +1,40 @@
+rule cnvkit_batch_build_reference:
+    input:
+        bam=["mapped/a.bam"],
+        bai=["mapped/a.bam.bai"],
+        fasta="ref/ref.fa",
+        antitarget="ref/a.antitarget.bed",
+        target="ref/a.target.bed",
+    output:
+        reference="cnvkit/reference.cnn",
+    log:
+        "cnvkit/a.reference.cnn.log",
+    params:
+        method='hybrid',  # optional
+        extra="--target-avg-size 10",  # optional
+    resources:
+        mem_mb=1024,
+    wrapper:
+        "master/bio/cnvkit/batch"
+
+rule cnvkit_batch:
+    input:
+        bam=["mapped/a.bam"],
+        bai=["mapped/a.bam.bai"],
+        reference="ref/reference.cnn",
+    output:
+        antitarget_coverage="cnvkit/a.antitargetcoverage.cnn",
+        bins="cnvkit/a.bintest.cns",
+        regions="cnvkit/a.cnr",
+        segments="cnvkit/a.cns",
+        segments_called="cnvkit/a.call.cns",
+        target_coverage="cnvkit/a.targetcoverage.cnn",
+    log:
+        "cnvkit/a.antitargetcoverage.cnn.log",
+    params:
+        method='hybrid',  # optional
+        extra="",  # optional
+    resources:
+        mem_mb=1024,
+    wrapper:
+        "master/bio/cnvkit/batch"

bio/cnvkit/batch/test/ref/a.target.bed

@@ -0,0 +1,4 @@
+chrM	251	277	LSU-rRNA_Hsa	1000	.
+chrY	11170	11213	ALR/Alpha	1000	.
+chrY	14339	14355	LSU-rRNA_Hsa	1000	.
+chrY	14360	14378	BSR/Beta	1000	.

bio/cnvkit/batch/test/ref/ref.fa.fai

@@ -0,0 +1,2 @@
+chrM	16571	6	50	51
+chrY	24316	16915	50	51

bio/cnvkit/batch/test/ref/reference.cnn

@@ -0,0 +1,12 @@
+chromosome	start	end	gene	log2	depth	gc	rmask	spread
+chrY	11170	11180	ALR/Alpha	-0.70752	3	0.7		0.433631
+chrY	11180	11191	ALR/Alpha	-0.562765	3	0.545455		0.648245
+chrY	11191	11202	ALR/Alpha	-0.5	3	0.454545		0.7413
+chrY	11202	11213	ALR/Alpha	-0.644755	3.09091	0.454545		0.526686
+chrY	14339	14347	LSU-rRNA_Hsa	-0.5	4	0.625		0.7413
+chrY	14347	14355	LSU-rRNA_Hsa	-0.314015	4	0.125		1.01704
+chrY	14360	14369	BSR/Beta	-0.5	3.77778	0.222222		0.7413
+chrY	14369	14378	BSR/Beta	-0.5	4	1		0.7413
+chrM	251	259	LSU-rRNA_Hsa	0.185575	91.75	0.5		0.275133
+chrM	259	268	LSU-rRNA_Hsa	2.17584	81.6667	0.666667		3.2259
+chrM	268	277	LSU-rRNA_Hsa	2.11547	75.1111	0.555556		3.1364

bio/cnvkit/batch/wrapper.py

@@ -0,0 +1,79 @@
+__author__ = "Patrik Smeds"
+__copyright__ = "Copyright 2023, Patrik Smeds"
+__email__ = "patrik.smeds@scilifelab.uu.se"
+__license__ = "MIT"
+
+import logging
+from os import listdir
+from os.path import basename
+from os.path import dirname
+from os.path import join
+from tempfile import TemporaryDirectory
+import shutil
+from snakemake.shell import shell
+
+log = snakemake.log_fmt_shell(stdout=False, stderr=True)
+
+input_bam_files = f"{snakemake.input.bam}"
+
+target = ""
+antitarget = ""
+ref_fasta = ""
+reference_cnv = ""
+mappability = ""
+
+create_reference = snakemake.output.get("reference", False)
+if create_reference:
+    input_bam_files = f"-n {input_bam_files}"
+    ref_fasta = f"-f {snakemake.input.fasta}"
+    target = f"-t {snakemake.input.target}"
+    antitarget = f"-a {snakemake.input.antitarget}"
+
+    if "mappability" in snakemake.input:
+        mappability = f"-g {snakemake.input.mappability}"
+
+    if len(snakemake.output) > 1:
+        exception_message = (
+            "Only one output expected when creating a reference, multiple output "
+            f"files defined as output: [{snakemake.output}]"
+        )
+        raise Exception(exception_message)
+else:
+    reference_cnv = f"-r {snakemake.input.reference}"
+
+method = snakemake.params.get("method", "hybrid")
+if method:
+    method = f"-m {method}"
+
+extra = snakemake.params.get("extra", "")
+
+with TemporaryDirectory() as tmpdirname:
+    if create_reference:
+        output = f"--output-reference {join(tmpdirname, 'reference.cnn')}"
+        output_list = [snakemake.output.reference]
+    else:
+        output_list = [value for key, value in snakemake.output.items()]
+        output = f"-d {tmpdirname} "
+    shell(
+        "(cnvkit.py batch {input_bam_files} "
+        "{reference_cnv} "
+        "{method} "
+        "{ref_fasta} "
+        "{target} "
+        "{antitarget} "
+        "{output} "
+        "{extra}) {log}"
+    )
+
+    for output_file in output_list:
+        filename = basename(output_file)
+        parent = dirname(output_file)
+
+        try:
+            shutil.copy2(join(tmpdirname, filename), output_file)
+        except FileNotFoundError as e:
+            temp_files = listdir(tmpdirname)
+            logging.error(
+                f"Couldn't locate file {basename} possible files are {[basename(f) for f in temp_files]}"
+            )
+            raise e

test.py

@@ -1180,6 +1180,19 @@ def test_bwa_mapping_meta():
         ],
     )
 
+@skip_if_not_modified
+def test_cnvkit_batch_create_reference():
+    run(
+        "bio/cnvkit/batch",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "--use-conda",
+           "cnvkit/reference.cnn",
+        ],
+    )
+
 @skip_if_not_modified
 def test_cnvkit_call():
     run(
@@ -1249,6 +1262,24 @@ def test_cnvkit_antitarget():
         ],
     )
 
+@skip_if_not_modified
+def test_cnvkit_batch():
+    run(
+        "bio/cnvkit/batch",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "--use-conda",
+            "cnvkit/a.antitargetcoverage.cnn",
+            "cnvkit/a.bintest.cns",
+            "cnvkit/a.cnr",
+            "cnvkit/a.cns",
+            "cnvkit/a.call.cns",
+            "cnvkit/a.targetcoverage.cnn",
+        ],
+    )
+
 @skip_if_not_modified
 def test_cnvkit_target():
     run(