feat: add galah wrapper (#1754)

<!-- Ensure that the PR title follows conventional commit style (<type>:
<description>)-->
<!-- Possible types are here:
https://github.com/commitizen/conventional-commit-types/blob/master/index.json
-->

### Description

<!-- Add a description of your PR here-->

### QC
<!-- Make sure that you can tick the boxes below. -->

* [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: David Laehnemann <david.laehnemann@hhu.de>

bio/galah/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - galah =0.3.1

bio/galah/meta.yaml

@@ -0,0 +1,12 @@
+name: galah
+description: More scalable dereplication for metagenome assembled genomes 
+url: https://github.com/wwood/galah
+authors:
+  - Filipe G. Vieira
+input:
+  - FASTA files
+output:
+  - clusters: representative FASTA<TAB>member lines
+  - repres: paths to representative FAS files
+params:
+  - extra: additional program arguments

bio/galah/test/Snakefile

@@ -0,0 +1,25 @@
+rule galah_fas:
+    input:
+        fas=["fas/a.fa", "fas/b.fas.bz2", "fas/c.fasta.gz"],
+    output:
+        clusters="results.fas.tsv",
+        repres="results.fas.list",
+    log:
+        "logs/out.fas.log",
+    params:
+        extra="--precluster-ani 0.9 --ani 0.95",
+    threads: 2
+    resources:
+        mem_mb=50,
+    wrapper:
+        "master/bio/galah"
+
+
+use rule galah_fas as galah_fas_list with:
+    input:
+        fas_list="fas/a.fas_list",
+    output:
+        clusters="results.fas_list.tsv",
+        repres="results.fas_list.list",
+    log:
+        "logs/out.fas_list.log",

bio/galah/test/fas/a.fa

@@ -0,0 +1,30 @@
+>1
+ACGGCAT
+>2
+ACGGCAT
+>3
+ACGGCAT
+>4
+ACGGCAT
+>5
+ACGGCAT
+>6
+ACGGCAT
+>7
+ACGGCAT
+>8
+ACGGCAT
+>9
+ACGGCAT
+>10
+ACGGCAT
+>11
+ACGGCAT
+>12
+ACGGCAT
+>13
+ACGGCAT
+>14
+ACGGCAT
+>15
+ACGGCAT

bio/galah/test/fas/a.fas_list

@@ -0,0 +1,3 @@
+fas/a.fa
+fas/b.fas.bz2
+fas/c.fasta.gz

bio/galah/wrapper.py

@@ -0,0 +1,41 @@
+__author__ = "Filipe G. Vieira"
+__copyright__ = "Copyright 2023, Filipe G. Vieira"
+__license__ = "MIT"
+
+from snakemake.shell import shell
+
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
+
+
+fas = snakemake.input.get("fas", "")
+if fas:
+    fas = f"--genome-fasta-files {' '.join(fas)}"
+
+
+fas_list = snakemake.input.get("fas_list", "")
+if fas_list:
+    fas_list = f"--genome-fasta-list {fas_list}"
+
+
+clusters = snakemake.output.get("clusters", "")
+if clusters:
+    clusters = f"--output-cluster-definition {clusters}"
+
+
+repres = snakemake.output.get("repres", "")
+if repres:
+    repres = f"--output-representative-list {repres}"
+
+
+shell(
+    "galah cluster"
+    " --threads {snakemake.threads}"
+    " {fas}"
+    " {fas_list}"
+    " {extra}"
+    " {clusters}"
+    " {repres}"
+    " {log}"
+)

test.py

@@ -139,6 +139,24 @@ def run(wrapper, cmd, check_log=None):
             os.chdir(origdir)
 
 
+@skip_if_not_modified
+def test_galah():
+    run(
+        "bio/galah",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "--use-conda",
+            "-F",
+            "results.fas.tsv",
+            "results.fas.list",
+            "results.fas_list.tsv",
+            "results.fas_list.list",
+        ],
+    )
+
+
 @skip_if_not_modified
 def test_nonpareil():
     run(