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add missing option
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huzuner authored Nov 3, 2024
1 parent db38192 commit 430e556
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion workflow/rules/assembly.smk
Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@ rule order_contigs:
shadow:
"minimal"
shell:
" ragtag.py scaffold -C -o {params.outdir}/{wildcards.sample} {input.reference} {input.contigs} &&"
" ragtag.py scaffold -C -w -o {params.outdir}/{wildcards.sample} {input.reference} {input.contigs} &&"
" mv {params.outdir}/{wildcards.sample}/ragtag.scaffold.fasta {output} > {log} 2>&1"


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