Nextflow Registry | nf-core/hifiasm@0.0.0-6c4ed3a

nf-core/hifiasm @ 0.0.0-6c4ed3a

Whole-genome assembly using PacBio HiFi reads

genome assembly haplotype resolution phasing PacBio HiFi long reads

Latest version: 0.0.0-6c4ed3a

Total downloads: 15

Source: nf-core/modules

Authors: @sidorov-si @scorreard @mbeavitt @schmytzi @prototaxites

Maintainers: @sidorov-si @scorreard

Summary

Whole-genome assembly using PacBio HiFi reads

Get started

Add the following snippet to your workflow script to include this module.

include { HIFIASM } from 'nf-core/hifiasm'

License

MIT License

Process

`Name`	`HIFIASM`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`long_reads` file	Long reads PacBio HiFi reads or ONT reads (requires ext.arg '--ont').
`ul_reads` file	ONT long reads to use with --ul.

#2 tuple

`meta2` map	Groovy Map containing information about parental kmers.
`paternal_kmer_dump` file	Yak kmer dump file for paternal reads (can be used for haplotype resolution). It can have an arbitrary extension.
`maternal_kmer_dump` file	Yak kmer dump file for maternal reads (can be used for haplotype resolution). It can have an arbitrary extension.

#3 tuple

`meta3` map	Groovy Map containing information about Hi-C reads
`hic_read1` file	Hi-C data Forward reads.
`hic_read2` file	Hi-C data Reverse reads.

#4 tuple

`meta4` map	Groovy Map containing information about the input bin files
`bin_files` file	bin files produced during a previous Hifiasm run

Output 11 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.stderr.log` file	Stderr log `*.stderr.log`

#2 bin_files tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bin` file	Binary files containing processed data for hifiasm, including error-corrected reads, read overlaps, and Hi-C alignments. Can be re-used as an input for subsequent re-runs of hifiasm with new inputs or modified parameters in order to save recomputation of initial results, which are the most computationally-expensive steps. `*.bin`

#3 raw_unitigs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.r_utg.gfa` file	Raw unitigs `*.r_utg.gfa`

#4 hap1_contigs tuple

meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

${prefix}.*.hap1.p_ctg.gfa file

Contigs for the first haplotype. How the haplotypes are represented depends on the input mode; in standard HiFi-only mode, these are partially-phased parental contigs. In Hi-C mode, they are fully phased parental contigs, but the phasing is not maintained between contigs. In trio mode, they are fully phased paternal contigs all originating from a single parental haplotype.

${prefix}.*.hap1.p_ctg.gfa

#5 hap2_contigs tuple

meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

${prefix}.*.hap2.p_ctg.gfa file

Contigs for the second haplotype. How the haplotypes are represented depends on the input mode; in standard HiFi-only mode, these are partially-phased parental contigs. In Hi-C mode, they are fully phased parental contigs, but the phasing is not maintained between contigs. In trio mode, they are fully phased paternal contigs all originating from a single parental haplotype.

${prefix}.*.hap2.p_ctg.gfa

#6 read_overlaps tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.ovlp.paf.gz` file	If option --write-paf specified, a gzipped paf file describing the overlaps among all error-corrected reads `*.ovlp.paf.gz`

#7 corrected_reads