perf: autobump bio/muscle (#612)

Automatic update of bio/muscle.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>

bio/muscle/environment.yaml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - muscle ==3.8.1551
+  - muscle =5.1

bio/muscle/meta.yaml

@@ -1,10 +1,12 @@
 name: muscle
-description: build multiple sequence alignments using MUSCLE. Documentation found at https://www.drive5.com/muscle/manual/index.html
+description: build multiple sequence alignments using MUSCLE.
+url: https://drive5.com/muscle5/manual/
 authors:
   - Nikos Tsardakas Renhuldt
 input:
   - FASTA file
 output:
   - Alignment file, with FASTA as default file format
-notes: |
-  * MUSCLE is a single-core program. It cannot utilize more than 1 thread.
+params:
+  - super5: specifies whether to use the Super5 algorithm to align sequences
+

bio/muscle/test/Snakefile

@@ -2,23 +2,26 @@ rule muscle_fasta:
     input:
         fasta="{sample}.fa",  # Input fasta file
     output:
-        alignment="{sample}.afa",  # Output alignment file
+        alignment="{sample}.fas",  # Output alignment file
     log:
         "logs/muscle/{sample}.log",
     params:
-        extra="",  # Additional arguments
+        extra="-refineiters 50",  # Additional arguments
+    threads: 2
     wrapper:
         "master/bio/muscle"
 
 
-rule muscle_clw:
+rule muscle_super5:
     input:
         fasta="{sample}.fa",
     output:
-        alignment="{sample}.clw",
+        alignment="{sample}.super5.fas",
     log:
-        "logs/muscle/{sample}.log",
+        "logs/muscle/{sample}.super5.log",
     params:
-        extra="-clw",
+        super5 = True,
+        extra="-refineiters 50",
+    threads: 2
     wrapper:
         "master/bio/muscle"

bio/muscle/wrapper.py

@@ -9,10 +9,15 @@
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 extra = snakemake.params.get("extra", "")
 
+mode = "-align"
+if snakemake.params.get("super5"):
+    mode = "-super5"
+
 shell(
-    "muscle "
-    "{extra} "
-    "-in {snakemake.input.fasta} "
-    "-out {snakemake.output.alignment} "
-    "{log}"
+    "muscle"
+    " -threads {snakemake.threads}"
+    " {mode} {snakemake.input.fasta}"
+    " {extra}"
+    " -output {snakemake.output.alignment}"
+    " {log}"
 )

test.py

@@ -2611,18 +2611,18 @@ def test_multiqc_a():
 
 
 @skip_if_not_modified
-def test_muscle_clw():
+def test_muscle_super5():
     run(
         "bio/muscle",
-        ["snakemake", "--cores", "1", "test-proteins.clw", "--use-conda", "-F"],
+        ["snakemake", "--cores", "2", "test-proteins.super5.fas", "--use-conda", "-F"],
     )
 
 
 @skip_if_not_modified
-def test_muscle_fa():
+def test_muscle_fas():
     run(
         "bio/muscle",
-        ["snakemake", "--cores", "1", "test-proteins.afa", "--use-conda", "-F"],
+        ["snakemake", "--cores", "2", "test-proteins.fas", "--use-conda", "-F"],
     )