fix: indexed bam files can now be put as input (#1378)

The program needs an indexed bam file but when the bai file is put in
input in the Snakemake rule it will be used as a --resource and the
program crashes. This fixes this bug.

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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/gatk/variantannotator/test/Snakefile

@@ -2,6 +2,7 @@ rule gatk_annotator:
     input:
         vcf="calls/snvs.vcf.gz",
         aln="mapped/a.bam",
+        bai="mapped/a.bam.bai",
         ref="genome.fasta",
         db="calls/snvs.vcf.gz",
 #        intervals="targets.bed",

bio/gatk/variantannotator/wrapper.py

@@ -32,7 +32,7 @@
 resources = [
     f"--resource:{name} {file}"
     for name, file in snakemake.input.items()
-    if name not in ["vcf", "aln", "ref", "known", "intervals"]
+    if name not in ["vcf", "aln", "ref", "known", "intervals", "bai"]
 ]