fix: add threads to trim_galore (#1452)

### Description

Add multiple threads option to trim_galore. 

### QC

* [ ] 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/trim_galore/pe/test/Snakefile

@@ -6,6 +6,7 @@ rule trim_galore_pe:
         "trimmed/{sample}.1.fastq.gz_trimming_report.txt",
         "trimmed/{sample}.2_val_2.fq.gz",
         "trimmed/{sample}.2.fastq.gz_trimming_report.txt",
+    threads: 1
     params:
         extra="--illumina -q 20",
     log:

bio/trim_galore/pe/wrapper.py

@@ -41,6 +41,7 @@
 shell(
     "(trim_galore"
     " {snakemake.params.extra}"
+    " --cores {snakemake.threads}"
     " --paired"
     " -o {out_dir}"
     " {snakemake.input})"

bio/trim_galore/se/test/Snakefile

@@ -6,6 +6,7 @@ rule trim_galore_se:
         "trimmed/{sample}.fastq.gz_trimming_report.txt",
     params:
         extra="--illumina -q 20",
+    threads: 1
     log:
         "logs/trim_galore/{sample}.log",
     wrapper:

bio/trim_galore/se/wrapper.py

@@ -37,6 +37,7 @@
 shell(
     "(trim_galore"
     " {snakemake.params.extra}"
+    " --cores {snakemake.threads}"
     " -o {out_dir}"
     " {snakemake.input})"
     " {log}"