name: hifiasm description: Whole-genome assembly using PacBio HiFi reads keywords: - genome assembly - haplotype resolution - phasing - PacBio - HiFi - long reads tools: - hifiasm: description: Haplotype-resolved assembler for accurate HiFi reads homepage: https://github.com/chhylp123/hifiasm documentation: https://github.com/chhylp123/hifiasm tool_dev_url: https://github.com/chhylp123/hifiasm doi: "10.1038/s41592-020-01056-5" licence: ["MIT"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file description: FASTQ file with PacBio HiFi reads pattern: "*.{fastq}" - paternal_kmer_dump: type: file description: Yak kmer dump file for paternal reads (can be used for haplotype resolution). It can have an arbitrary extension. - maternal_kmer_dump: type: file description: Yak kmer dump file for maternal reads (can be used for haplotype resolution). It can have an arbitrary extension. - use_parental_kmers: type: logical description: A flag (true or false) signalling if the module should use the paternal and maternal kmer dumps. output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - version: type: file description: File containing software version pattern: "*.{version.txt}" - raw_unitigs: type: file description: Raw unitigs pattern: "*.r_utg.gfa" - processed_unitigs: type: file description: Processed unitigs pattern: "*.p_utg.gfa" - primary_contigs: type: file description: Primary contigs pattern: "*.asm.p_ctg.gfa" - alternate_contigs: type: file description: Alternative contigs pattern: "*.asm.a_ctg.gfa" - paternal_contigs: type: file description: Paternal contigs pattern: "*.hap1.p_ctg.gfa" - maternal_contigs: type: file description: Maternal contigs pattern: "*.hap2.p_ctg.gfa" - corrected_reads: type: file description: Corrected reads pattern: "*.ec.bin" - source_overlaps: type: file description: Source overlaps pattern: "*.ovlp.source.bin" - reverse_overlaps: type: file description: Reverse overlaps pattern: "*.ovlp.reverse.bin" authors: - "@sidorov-si"