fix: deeptools bamcoverage fix (#2719)

Fixes a small issue when including the genome and read_length pulling
from the pre-computed effective genome sizes. The returned genome size
is an int rather than a string.

### 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),
* the `environment.yaml` pinning has been updated by running
`snakedeploy pin-conda-envs environment.yaml` on a linux machine,
* 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/deeptools/bamcoverage/test/Snakefile

@@ -13,3 +13,18 @@ rule test_deeptools_bamcoverage:
         "logs/coverage.log",
     wrapper:
         "master/bio/deeptools/bamcoverage"
+
+
+rule test_deeptools_bamcoverage_default_eff_len:
+    input:
+        bam="a.sorted.bam",
+        bai="a.sorted.bam.bai",
+    output:
+        "a.coverage_code.bw",
+    params:
+        genome="GRCm38",
+        read_length=200,
+    log:
+        "logs/coverage_efault_eff_len.log",
+    wrapper:
+        "master/bio/deeptools/bamcoverage"

bio/deeptools/bamcoverage/wrapper.py

@@ -10,61 +10,93 @@
 
 # See: https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
 default_effective_genome_size = {
-    "GRCz10": {
-        "50": 1195445591,
-        "75": 1251132686,
-        "100": 1280189044,
-        "150": 1312207169,
-        "200": 1321355241,
-    },
-    "WBcel235": {
-        "50": 95159452,
-        "75": 96945445,
-        "100": 98259998,
-        "150": 98721253,
-        "200": 98672758,
-    },
-    "dm3": {
-        "50": 130428560,
-        "75": 135004462,
-        "100": 139647232,
-        "150": 144307808,
-        "200": 148524010,
-    },
-    "dm6": {
-        "50": 125464728,
-        "75": 127324632,
-        "100": 129789873,
-        "150": 129941135,
-        "200": 132509163,
-    },
     "GRCh37": {
-        "50": 2685511504,
-        "75": 2736124973,
-        "100": 2776919808,
-        "150": 2827437033,
-        "200": 2855464000,
+        "50": 2685511454,
+        "75": 2736124898,
+        "100": 2776919708,
+        "150": 2827436883,
+        "200": 2855463800,
+        "250": 2855044784,
     },
     "GRCh38": {
-        "50": 2701495761,
-        "75": 2747877777,
-        "100": 2805636331,
-        "150": 2862010578,
-        "200": 2887553303,
+        "50": 2701495711,
+        "75": 2747877702,
+        "100": 2805636231,
+        "150": 2862010428,
+        "200": 2887553103,
+        "250": 2898802627,
     },
     "GRCm37": {
-        "50": 2304947926,
-        "75": 2404646224,
-        "100": 2462481010,
-        "150": 2489384235,
-        "200": 2513019276,
+        "50": 2304947876,
+        "75": 2404646149,
+        "100": 2462480910,
+        "150": 2489384085,
+        "200": 2513019076,
+        "250": 2528988583,
     },
     "GRCm38": {
-        "50": 2308125349,
-        "75": 2407883318,
-        "100": 2467481108,
-        "150": 2494787188,
-        "200": 2520869189,
+        "50": 2308125299,
+        "75": 2407883243,
+        "100": 2467481008,
+        "150": 2494787038,
+        "200": 2520868989,
+        "250": 2538590322,
+    },
+    "GRCz10": {
+        "50": 1195445541,
+        "75": 1251132611,
+        "100": 1280188944,
+        "150": 1312207019,
+        "200": 1321355041,
+        "250": 1339205109,
+    },
+    "GRCz11": {
+        "50": 1197575653,
+        "75": 1250812288,
+        "100": 1280354977,
+        "150": 1311832909,
+        "200": 1322366338,
+        "250": 1342093482,
+    },
+    "T2T/CHM13CAT_v2": {
+        "50": 2725240337,
+        "75": 2786136059,
+        "100": 2814334875,
+        "150": 2931551487,
+        "200": 2936403235,
+        "250": 2960856300,
+    },
+    "TAIR10": {
+        "50": 114339094,
+        "75": 115317469,
+        "100": 118459858,
+        "150": 118504138,
+        "200": 117723393,
+        "250": 119585546,
+    },
+    "WBcel235": {
+        "50": 95159402,
+        "75": 96945370,
+        "100": 98259898,
+        "150": 98721103,
+        "200": 98672558,
+        "250": 101271756,
+    },
+    "dm3": {
+        "50": 130428510,
+        "75": 135004387,
+        "100": 139647132,
+        "150": 144307658,
+        "200": 148523810,
+        "250": 151901455,
+    },
+    "dm6": {
+        "50": 125464678,
+        "75": 127324557,
+        "100": 129789773,
+        "150": 129940985,
+        "200": 132508963,
+        "250": 132900923,
     },
 }
 
@@ -73,10 +105,17 @@
     genome = snakemake.params.get("genome")
     read_length = snakemake.params.get("read_length")
     if genome and read_length:
-        effective_genome_size = "--effectiveGenomeSize "
-        effective_genome_size += default_effective_genome_size[genome][str(read_length)]
+        try:
+            effective_genome_size = f"--effectiveGenomeSize {default_effective_genome_size[genome][str(read_length)]}"
+        except KeyError:
+            raise KeyError(
+                (
+                    "A valid genome and read_length need to be provided. See "
+                    "https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html"
+                )
+            )
 else:
-    effective_genome_size = "--effectiveGenomeSize " + str(effective_genome_size)
+    effective_genome_size = f"--effectiveGenomeSize {effective_genome_size}"
 
 
 output_format = ""

test.py

@@ -2833,6 +2833,21 @@ def test_deeptools_bamcoverage():
     )
 
 
+@skip_if_not_modified
+def test_deeptools_bamcoverage_eff():
+    run(
+        "bio/deeptools/bamcoverage",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "a.coverage_code.bw",
+            "--use-conda",
+            "-F",
+        ],
+    )
+
+
 @skip_if_not_modified
 def test_deeptools_alignmentsieve():
     run(