Description

Build a gzipped Juicer .pairs file from a sorted alignment table and juicerc log — combining the zippypretext make_header.sh and makepairs.sh steps.

Input

Name
Description
Pattern

meta (map)

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

alignment (file)

Sorted alignment table from juicerc (*_alignment_sorted.txt)

*_alignment_sorted.txt

outlog (file)

Log file from juicerc containing PRE_C_SIZE chromosome entries

juicercout.log

Output

Name
Description
Pattern

pairs

meta (map)

Groovy Map containing sample information

*_alignment.pairs.gz (file)

Gzipped pairs file for pretextmap

*_alignment.pairs.gz

versions_pretext_makepairs

${task.process} (string)

The process the versions were collected from

pretext_makepairs (string)

The tool name

1.0.0 (string)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The process the versions were collected from

pretext_makepairs (string)

The tool name

1.0.0 (string)

The expression to obtain the version of the tool

Tools

pretext_makepairs Documentation

Parse chromosome sizes from juicercout.log (PRE_C_SIZE lines) to write the pairs header, append alignment rows from JUICERC output, and gzip the result. Output filename uses task.ext.prefix (default meta.id), e.g. sample_alignment.pairs.gz.

License: MIT
Authors