feat: Lofreq indelqual wrapper (#1166)

### Description
Snakemake wrapper for the tool lofreq. Specifically the lofreq indelqual
portion of the tool.

### QC

* [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/lofreq/indelqual/environment.yaml

@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - samtools =1.16.1
+  - lofreq =2.1.3.1

bio/lofreq/indelqual/meta.yaml

@@ -0,0 +1,12 @@
+name: lofreq indelqual
+description: Insert indel qualities into BAM file (required for indel predictions)
+url: https://csb5.github.io/lofreq/
+authors:
+  - Tobin Groth
+input:
+  - bam file that will have variants called
+  - reference genome of bam (optional unless --dindel specified)
+output:
+  - bam file with indel qualities added
+params (optional):
+  - extra: additional paramters (e.g.) `--uniform INT[,INT]` (uniform quality), or `--dindel` (dindel's indel qualities).

bio/lofreq/indelqual/test/Snakefile

@@ -0,0 +1,12 @@
+rule lofreq_indelqual:
+    input:
+        bam="data/{sample}.bam",
+    output:
+        "out/indelqual/{sample}.indel.bam"
+    log:
+        "logs/{sample}.log"
+    params:
+        extra="-u 15"
+    threads: 8
+    wrapper:
+        "master/bio/lofreq/indelqual"