fix!: trimmomatic wrappers: remove parallel gzip, merge wrappers, added docs, and code refactoring. (#4158)

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Current parallel compression/decompression with `pigz` is no longer
supported in latest versions of `Trimmomatic` and it breaks MultiQC
reporting. Since it seems that the next version of Trimmomatic will have
[parallel compression](

usadellab/Trimmomatic@7220eba),
this issues removes it, bumps versions, refactors code, merges the two
PE/SE wrappers, and iproves docs.

Closes #778 
Closes #869 
Fixes #961 

### QC
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* [x] I confirm that I have followed the [documentation for contributing
to
`snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html).

While the contributions guidelines are more extensive, please
particularly ensure that:
* [x] `test.py` was updated to call any added or updated example rules
in a `Snakefile`
* [x] `input:` and `output:` file paths in the rules can be chosen
arbitrarily
* [x] wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`)
* [x] 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
* [x] the `meta.yaml` contains a link to the documentation of the
respective tool or command under `url:`
* [x] conda environments use a minimal amount of channels and packages,
in recommended ordering


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Introduced unified configuration and metadata files for running
Trimmomatic, supporting both paired-end and single-end workflows with
various input/output formats.
- Added a new wrapper script to streamline Trimmomatic execution within
Snakemake workflows.

- **Refactor**
- Consolidated multiple environment and metadata files into a single set
for easier management and reproducibility.
- Unified Snakemake rules for Trimmomatic into a single, comprehensive
Snakefile covering all compression and read-type combinations.
- Removed legacy single-end and paired-end specific environment and
metadata files along with deprecated wrapper scripts.

- **Tests**
- Simplified and consolidated test coverage for paired-end workflows;
removed separate single-end tests.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Author: fgvieira

bio/trimmomatic/environment.linux-64.pin.txt

@@ -0,0 +1,79 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+# created-by: conda 25.5.0
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bio/trimmomatic/environment.yaml

@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - trimmomatic =0.39
+  - snakemake-wrapper-utils =0.7.2

bio/trimmomatic/meta.yaml

@@ -0,0 +1,20 @@
+name: "trimmomatic pe"
+description: Trim reads with Trimmomatic.
+url: http://www.usadellab.org/cms/?page=trimmomatic
+authors:
+  - Johannes Köster
+  - Jorge Langa
+  - Filipe G. Vieira
+input:
+  - r1: fastq(gz) file
+  - r2: fastq(gz) file (if PE)
+output:
+  - r1: trimmed R1 fastq(gz) file 
+  - r2: trimmed R2 fastq(gz) file (if PE)
+  - r1_unpaired: unpaired R1 fastq(gz) file (if PE)
+  - r2_unpaired: unpaired R2 fastq(gz) file (if PE)
+params:
+  - trimmer: trimming steps
+  - extra: additional program arguments
+notes: |
+  For PE (paired-end) trimming, all output files need to be specified.