Performs assembly scaffolding using YaHS
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
fasta
:file
FASTA reference file
*.{fasta,fa}
fai
index of the reference file
*.{fai}
hic_map
BED file containing coordinates of read alignments
*.{bed,bam,bin}
agp
Optional AGP file describing a set of scaffolds from the input contigs to use as a start point
*.agp
scaffolds_fasta
${prefix}_scaffolds_final.fa
FASTA file with resulting contigs
scaffolds_agp
${prefix}_scaffolds_final.agp
AGP file containing contigs placing coordinates
initial_break_agp
${prefix}_{inital,no}_break*.agp
AGP file describing initial contig breaks
round_agp
${prefix}_r*_*.agp
AGP file describing intermediate rounds of scaffolding
${prefix}_{initial,no}_break*.agp
binary
${prefix}.bin
Binary data file with alignment results of Hi-C reads to the contigs in internal YaHS binary format
log
${prefix}.log
Log file describing YaHS run
versions_yahs
${task.process}
:string
The name of the process
yahs
The name of the tool
yahs --version 2>&1
:eval
The expression to obtain the version of the tool
versions
YaHS, yet another Hi-C scaffolding tool.
