Description

Generate a params file in json format for sanger-tol/curationpretext

Input

Name
Description
Pattern

meta (map)

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

reference (file)

Input assembly fasta file

[*.{fasta,fa,fna}]

longread_dir (directory)

Directory containing longread fa(asta).gz files

cram_dir (directory)

Directory containing hic cram files

telomere_motif (string)

A telomere motif string

aligner (string)

Aligner to be used (minimap2, bwamem2, AUTO)

cpretext_extra_opts (map)

Map of extra arguments for curationpretext

Output

Name
Description
Pattern

json_params_file

meta (map)

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

*.json (file)

JSON params file required for CurationPretext

versions_curationpretextgenerateparamsfile

${task.process} (string)

The name of the process

curationpretext_generateparamsfile (string)

The name of the tool

1.0.0 (string)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The name of the process

curationpretext_generateparamsfile (string)

The name of the tool

1.0.0 (string)

The expression to obtain the version of the tool

Tools

curationpretext_generateparamsfile Documentation

A samplesheet generator for the CurationPretext pipeline

https://pipelines.tol.sanger.ac.uk/curationpretext/usagedoi: 10.5281/zenodo.12773958
Authors