diff --git a/workflow/rules/purge_dups.smk b/workflow/rules/purge_dups.smk index 82eac98..b8ba7b2 100644 --- a/workflow/rules/purge_dups.smk +++ b/workflow/rules/purge_dups.smk @@ -25,7 +25,7 @@ rule run_purge_dups: minimap2 -xasm20 {input.fasta} {input.reads} -t {config[minimap2][t]} | gzip -c - > hifi_vs_hifiasm_contigs.paf.gz >> {log} 2>&1 pbcstat hifi_vs_hifiasm_contigs.paf.gz >> {log} 2>&1 calcuts PB.stat > cutoffs 2>calcults.log - split_fa results/assemblies/hifiasm/hifiasm.asm.bp.p_ctg.fa > hifiasm.asm.split >> {log} 2>&1 + split_fa results/assemblies/hifiasm/hifiasm.asm.p_ctg.fa > hifiasm.asm.split >> {log} 2>&1 minimap2 -xasm5 -DP hifiasm.asm.split hifiasm.asm.split -t {config[minimap2][t]} | gzip -c - > hifiasm.split.self.paf.gz >> {log} 2>&1 purge_dups -2 -T cutoffs -c PB.base.cov hifiasm.split.self.paf.gz > dups.bed 2> purge_dups.log get_seqs -e dups.bed results/hifiasm/hifiasm.asm.bp.p_ctg.fa > hifiasm_p_purged.fa >> {log} 2>&1