Snakefile "ymp/rules/prodigal.rules"
Env(name="prodigal", base="bioconda", packages="prodigal")
with Stage("annotate_prodigal") as S:
S.doc("""
Call genes using prodigal
>>> ymp make toy.ref_genome.annotate_prodigal
""")
S.add_param(key="", typ="choice", name="procedure",
value=["S","M"], default="M")
S.add_param(key="G", typ="int", name="translation_table",
default=11)
rule prodigal:
"""Predict genes using prodigal"""
message:
"Gene prediction (Prodigal): {input}"
input:
"{:prev:}/{:target:}.fasta.gz"
output:
gtf = "{:this:}/{target}.gtf"
log:
"{:this:}/{target}.log"
threads: 1
conda:
"prodigal"
shell: """
gunzip -c {input} | \
prodigal -p meta \
-f gff -o {output.gtf} \
>{log} 2>&1
"""
#-d >(gzip -c9 > {output.fna}) \
#-a >(gzip -c9 > {output.faa}) \