feat: Goleft indexcov (snakemake#2734)

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THis PR add [goleft
indexcov](https://github.com/brentp/goleft/tree/master/indexcov) to the
list of available wrappers.

### 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),
* 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: tdayris <[email protected]>
Co-authored-by: tdayris <[email protected]>
Co-authored-by: Johannes Köster <[email protected]>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Co-authored-by: Felix Mölder <[email protected]>
Co-authored-by: Christopher Schröder <[email protected]>
Co-authored-by: Filipe G. Vieira <[email protected]>

Author: 9 people

bio/goleft/indexcov/environment.linux-64.pin.txt

@@ -0,0 +1,28 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.27.0-hd590300_0.conda#f6afff0e9ee08d2f1b897881a4f38cdb
+https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda#6aa9c9de5542ecb07fdda9ca626252d8
+https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_0.conda#51a753e64a3027bd7e23a189b1f6e91e
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
+https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
+https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
+https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
+https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.5.0-hca28451_0.conda#7144d5a828e2cae218e0e3c98d8a0aeb
+https://conda.anaconda.org/bioconda/linux-64/htslib-1.19.1-h81da01d_2.tar.bz2#ad57eedd99d6722b2f00a8f7d0d71e2a
+https://conda.anaconda.org/bioconda/linux-64/samtools-1.19.2-h50ea8bc_1.tar.bz2#446e85653117e24527bc4ba6d3841d8b
+https://conda.anaconda.org/bioconda/linux-64/goleft-0.2.4-h9ee0642_1.tar.bz2#a8658992b88c9323cff55ea1237a7103

bio/goleft/indexcov/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - goleft=0.2.4

bio/goleft/indexcov/meta.yaml

@@ -0,0 +1,19 @@
+name: "goleft indexcov"
+description: "Quickly estimate coverage from a whole-genome bam or cram index"
+url: "https://github.com/brentp/goleft/tree/master/indexcov#indexcov"
+authors:
+  - "Thibault Dayris"
+input:
+  - aln: Path to indexed BAM/CRAM file
+  - fai: Path to fasta sequence index
+output:
+  - html: Optional path to HTML report
+  - bed: Optional path to coverage bed
+  - ped: Optional path to pedigree file
+  - roc: Optional path to coverage curves
+params:
+  - extra: Optional parameters besides `-d` or `-r`
+notes: |
+  Coverage bed, pedigree file, and roc curves are available in the HTML report.
+  Using `bed`, `ped`, or `roc` output keys alongside with `html` will make these
+  results unavailable in the HTML report, but won't break HTML content display.

bio/goleft/indexcov/test/Snakefile

@@ -0,0 +1,15 @@
+rule test_goleft_indexcov:
+    input:
+        aln="sample.bam",
+        fai="genome.fai",
+    output:
+        bed="regions.bed.gz",
+        ped="indexcov.ped",
+        roc="indexcov.roc",
+        html=directory("report"),
+    log:
+        "indexcov.log",
+    params:
+        extra="-e",
+    wrapper:
+        "master/bio/goleft/indexcov"

bio/goleft/indexcov/test/genome.fai

@@ -0,0 +1,20 @@
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+2	243199373	253404903	60	61
+3	198022430	500657651	60	61
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+7	159138663	1254218344	60	61
+8	146364022	1416009371	60	61
+9	141213431	1564812846	60	61
+10	135534747	1708379889	60	61
+11	135006516	1846173603	60	61
+12	133851895	1983430282	60	61
+13	115169878	2119513096	60	61
+14	107349540	2236602526	60	61
+15	102531392	2345741279	60	61
+16	90354753	2449981581	60	61
+17	81195210	2541842300	60	61
+18	78077248	2624390817	60	61
+19	59128983	2703769406	60	61
+20	63025520	2763883926	60	61