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updating hifiasm output name
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LiaOb21 committed Jan 3, 2024
1 parent 4a1b24d commit 79fd486
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion workflow/rules/purge_dups.smk
Original file line number Diff line number Diff line change
Expand Up @@ -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
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