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