mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
87 lines
2.5 KiB
YAML
87 lines
2.5 KiB
YAML
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 ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- 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"
|