Snakefile "ymp/rules/align.rules"
rule combine_with_ref:
message:
"Adding {wildcards.gene} reference sequences to {input[1]}"
input:
"{gene}_ref.fastp",
"{dir}/{query}.{gene}.e{evalue}.fastp"
output:
"{dir}/{query}.{gene}.e{evalue}.with_ref.fastp.gz"
shell:
"zcat {input} | gzip -c > {output}"
rule align_mafft:
message:
"MaFFT aligning {input}"
input:
"{dir}/{file}.fastp"
output:
"{dir}.mafft/{file}.aligned.fastp.gz"
log:
"{dir}.mafft/{file}.log"
threads:
32
shell:"""
cat {input} | \
mafft \
--maxiterate 1000 \
--localpair \
--reorder \
--thread {threads} \
- \
2> {log} | gzip -c > {output}
"""