assembly w/ operams: added perl for execution (issue #40), minor change of rule name

workflow/rules/assembly.smk

@@ -145,7 +145,7 @@ rule assemble_hy_metaspades:
         "cd $(dirname {output}) && ln -sf contigs.fasta $(basename {output}) && "
         "date) 2> {log.err} > {log.out}"
 
-rule assemble_hy_operams:
+rule assembly_hy_operams:
     input: 
         lr=os.path.join(RESULTS_DIR, "preproc/metag/lr/lr.fastq.gz"),
         r1=os.path.join(RESULTS_DIR, "preproc/metag/sr/R1.fastp.fastq.gz"),
@@ -166,7 +166,7 @@ rule assemble_hy_operams:
     shell:
        "(date && "
        "zcat {input.lr} > {output.lr} && "
-       "{config[operams][bin]} --short-read1 {input.r1} --short-read2 {input.r2} --long-read {output.lr} --contig-file {input.asm} "
+       "perl {config[operams][bin]} --short-read1 {input.r1} --short-read2 {input.r2} --long-read {output.lr} --contig-file {input.asm} "
        "--out-dir $(dirname {output.asm}) --long-read-mapper minimap2 --num-processors {threads} && "
        "cd $(dirname {output.asm}) && ln -sf contigs.fasta $(basename {output.asm}) && "
        "date) 2> {log.err} > {log.out}"
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