Description

Wrapper around the YaHS juicer_pre tool to create a valid sorted pairs file describing Hi-C contacts among scaffolds using contacts among contigs and the YaHS AGP file describing the makeup of scaffolds from those contigs.

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

scaffolds_fai (file)

samtools fasta index files describing the scaffolds to make a pairs file for

*.fai

scaffolds_agp (file)

AGP file describing the mapping of raw contigs to scaffolds

*.agp

contigs_fai (file)

samtools fasta index files describing the scaffolds to make a pairs file for

*.fai

contigs_contacts (file)

Supported file format (BAM, BED, pairs, YaHS binary) describing Hi-C contacts between contigs

*.{bam,bed,bin,pa5}

Output

Name
Description
Pattern

pairs

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.pairs.gz (file)

Pairs file describing Hi-C contacts between scaffolds

*.pairs.gz

versions_gawk

${task.process} (string)

The name of the process

gawk (string)

The name of the tool

awk -Wversion | sed "1!d; s/.*Awk //; s/,.*//" (eval)

The expression to obtain the version of the tool

versions_sort

${task.process} (string)

The name of the process

sort (string)

The name of the tool

sort --version | grep -o -E "[0-9]+(\.[0-9]+)+" (eval)

The expression to obtain the version of the tool

versions_juicerpre

${task.process} (string)

The name of the process

juicer_pre (string)

The name of the tool

juicer pre --version (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The name of the process

juicer_pre (string)

The name of the tool

juicer pre --version (eval)

The expression to obtain the version of the tool

${task.process} (string)

The name of the process

gawk (string)

The name of the tool

awk -Wversion | sed "1!d; s/.*Awk //; s/,.*//" (eval)

The expression to obtain the version of the tool

${task.process} (string)

The name of the process

sort (string)

The name of the tool

sort --version | grep -o -E "[0-9]+(\.[0-9]+)+" (eval)

The expression to obtain the version of the tool

Tools

yahs Documentation

YaHS, yet another Hi-C scaffolding tool.

doi: 10.1093/bioinformatics/btac808License: MIT
Pipelines with this module
genomeassembly
Authors