feat: add MUSCLE wrapper (#404)

* Add muscle wrapper

* Comment and lint MUSCLE Snakefile

* Remove colon from MUSCLE meta.yaml

* Remove thread from muscle snakefile

bio/muscle/environment.yaml

@@ -0,0 +1,5 @@
+channels:
+  - bioconda
+  - conda-forge
+dependencies:
+  - muscle ==3.8.1551

bio/muscle/meta.yaml

@@ -0,0 +1,10 @@
+name: muscle
+description: build multiple sequence alignments using MUSCLE. Documentation found at https://www.drive5.com/muscle/manual/index.html
+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.

bio/muscle/test/Snakefile

@@ -0,0 +1,24 @@
+rule muscle_fasta:
+    input:
+        fasta="{sample}.fa",  # Input fasta file
+    output:
+        alignment="{sample}.afa",  # Output alignment file
+    log:
+        "logs/muscle/{sample}.log",
+    params:
+        extra="",  # Additional arguments
+    wrapper:
+        "master/bio/muscle"
+
+
+rule muscle_clw:
+    input:
+        fasta="{sample}.fa",
+    output:
+        alignment="{sample}.clw",
+    log:
+        "logs/muscle/{sample}.log",
+    params:
+        extra="-clw",
+    wrapper:
+        "master/bio/muscle"

bio/muscle/test/test-proteins.fa

@@ -0,0 +1,10 @@
+>test_protein
+MVKYSREPDNPTKSCKARGSDLRVHFKNTRETAHAIRKMQLGKAKSYLEDVLAHKQAIPF
+RRFCRGVGRTAQAKNRQSNGQGRWPVKSANFILDLLKNAESNAEVKGLDVDSLYVSHIQV
+NQAQKQRRRTYRAHGRINPYMSSPCHIELVLSEKEEPVKKEPETQLAPRKSRKGQALHSG
+AS
+>test_protein2
+MVKSREPDNPTKSCKARGSDLRVHFKNTRETAHAIRKMQLGKAKSYLEDVLAHKQAIPFR
+RFCRGVGRTAQAKNRQSNGQGRWPVKSANFILDLLKNAESNAEVKGLDVDSLYVSHIQVN
+QAQKQRRRTYRAHGRINPYMSSPCHIELVLSEKEEPVKKEPETQLAPRKSRKGQALHSGA
+S

bio/muscle/wrapper.py

@@ -0,0 +1,18 @@
+__author__ = "Nikos Tsardakas Renhuldt"
+__copyright__ = "Copyright 2021, Nikos Tsardakas Renhuldt"
+__email__ = "nikos.tsardakas_renhuldt@tbiokem.lth.se"
+__license__ = "MIT"
+
+
+from snakemake.shell import shell
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
+
+shell(
+    "muscle "
+    "{extra} "
+    "-in {snakemake.input.fasta} "
+    "-out {snakemake.output.alignment} "
+    "{log}"
+)

test.py

@@ -2029,6 +2029,22 @@ def test_multiqc():
     )
 
 
+@skip_if_not_modified
+def test_muscle_clw():
+    run(
+        "bio/muscle",
+        ["snakemake", "--cores", "1", "test-proteins.clw", "--use-conda", "-F"],
+    )
+
+
+@skip_if_not_modified
+def test_muscle_fa():
+    run(
+        "bio/muscle",
+        ["snakemake", "--cores", "1", "test-proteins.afa", "--use-conda", "-F"],
+    )
+
+
 @skip_if_not_modified
 def test_nanosimh():
     run(