diff --git a/workflow/rules/long_read.smk b/workflow/rules/long_read.smk index 33e4cec0..44892e7d 100644 --- a/workflow/rules/long_read.smk +++ b/workflow/rules/long_read.smk @@ -133,7 +133,7 @@ rule clip_adbc_corrected: conda: "../envs/notramp.yaml" shell: - "notramp -t --incl_prim -r {input.reads} -p {input.primer} -g {input.ref_genome} -o {params.outdir} 2> {log}" + "notramp -t -r {input.reads} -p {input.primer} -g {input.ref_genome} -o {params.outdir} 2> {log}" rule bcftools_consensus_ont: