feat: added wrapper for seqtk seq subcommand (#202)

* added wrapper for seqtk seq subcommand

* added test and linted

bio/seqtk/seq/environment.yaml

@@ -0,0 +1,5 @@
+channels:
+  - bioconda
+  - conda-forge
+dependencies:
+  - seqtk ==1.3

bio/seqtk/seq/meta.yaml

@@ -0,0 +1,10 @@
+name: seqtk-seq
+description: |
+  Common transformations of FASTA/Q using seqtk
+url: https://github.com/lh3/seqtk
+authors:
+  - William Rowell
+input:
+  - fastn file (can be gzip compressed)
+output:
+  - fastn file (gzip compressed)

bio/seqtk/seq/test/Snakefile

@@ -0,0 +1,11 @@
+rule seqtk_seq_fastq_to_fasta:
+    input:
+        "{prefix}.fastq",
+    output:
+        "{prefix}.fasta",
+    log:
+        "{prefix}.log",
+    params:
+        extra="-A",
+    wrapper:
+        "master/bio/seqtk/seq"

bio/seqtk/seq/test/a.fastq

@@ -0,0 +1,4 @@
+@1
+ACGGCAT
++
+!!!!!!!

bio/seqtk/seq/wrapper.py

@@ -0,0 +1,15 @@
+"""Snakemake wrapper seqtk seq subcommand"""
+
+__author__ = "William Rowell"
+__copyright__ = "Copyright 2020, William Rowell"
+__email__ = "wrowell@pacb.com"
+__license__ = "MIT"
+
+
+from snakemake.shell import shell
+
+
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=False, stderr=True)
+
+shell("(seqtk seq {extra} {snakemake.input} > {snakemake.output}) {log}")

test.py

@@ -605,6 +605,14 @@ def test_shovill():
     )
 
 
+@skip_if_not_modified
+def test_seqtk_seq():
+    run(
+        "bio/seqtk/seq",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "a.fasta"],
+    )
+
+
 @skip_if_not_modified
 def test_seqtk_mergepe():
     run(