feat: bedtools split wrapper (#1744)

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### Description

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### QC
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* [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).

bio/bedtools/split/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - bedtools =2.31.0

bio/bedtools/split/meta.yaml

@@ -0,0 +1,15 @@
+name: bedtools split
+description: >
+  Splits a BED file balancing the number of subfiles not just by number of lines, but also by total number of base pairs in each sub file.
+url: https://bedtools.readthedocs.io/
+authors:
+  - Filipe G. Vieira
+input:
+  - bed: Path to BED file
+output:
+  - Several BED files
+params:
+  - extra: additional program arguments (except for `-i`, `-n`, or `-p`)
+notes: |
+  * This program/wrapper does not handle multi-threading.
+  * 'bedtools split' is currently undocumented, even though it was added to 'bedtools' on version `2.23.0` (https://bedtools.readthedocs.io/en/latest/content/history.html#version-2-23-0-22-feb-2015).

bio/bedtools/split/test/Snakefile

@@ -0,0 +1,17 @@
+
+scattergather:
+    n_bed=2,
+
+
+rule bedtools_split:
+    input:
+        bed="a.bed",
+    output:
+        scatter.n_bed("results/a.{scatteritem}.bed"),
+    log:
+        "logs/a.split.log",
+    params:
+        ## Add optional parameters for spliting order
+        extra="--algorithm size",
+    wrapper:
+        "master/bio/bedtools/split"

bio/bedtools/split/test/a.bed

@@ -0,0 +1,5 @@
+1	100	200
+1	150	250
+2	100	200
+2	150	250
+2	200	300

bio/bedtools/split/wrapper.py

@@ -0,0 +1,26 @@
+__author__ = "Filipe G. Vieira"
+__copyright__ = "Copyright 2023, Filipe G. Vieira"
+__license__ = "MIT"
+
+import tempfile
+from snakemake.shell import shell
+
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+n_subfiles = len(snakemake.output)
+
+with tempfile.TemporaryDirectory() as tmpdir:
+    shell(
+        "bedtools split"
+        " --input {snakemake.input.bed}"
+        " --number {n_subfiles}"
+        " {extra}"
+        " --prefix {tmpdir}/out"
+        " {log}"
+    )
+
+    for i in range(n_subfiles):
+        out_tmp = f"{tmpdir}/out.{i+1:05d}.bed"
+        out = snakemake.output[i]
+        shell("cat {out_tmp} > {out}")

test.py

@@ -1638,6 +1638,14 @@ def test_bedtools_sort():
         ],
     )
 
+
+@skip_if_not_modified
+def test_bedtools_split():
+    run(
+        "bio/bedtools/split",
+        ["snakemake", "--cores", "1", "results/a.1-of-2.bed", "results/a.2-of-2.bed", "--use-conda", "-F"],
+    )
+
 
 @skip_if_not_modified
 def test_bedtools_intersect():