diff --git a/workflow/rules/assembly.smk b/workflow/rules/assembly.smk index e48c9ba8364be936105c3dabedcae118df9a4190..64bff37c2f47e109f777acbb46ae5d9d2b8437a4 100644 --- a/workflow/rules/assembly.smk +++ b/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}" \ No newline at end of file