Description

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

Input

Name
Description
Pattern

meta (map)

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

reference (file)

Input assembly fasta file

[*.{fasta,fa,fna}]

blastp (file)

The Uniprot Diamond Protein Database for BlastP (aligning proteins to a protein database)

*.dmnd

blastn (directory)

The NCBI Nucleotide database path for BlastN (aligning nucleotides to a nucleotide database)

blastx (file)

The Uniprot Diamond Protein Database path for BlastX (aligning nucleotides to a protein database)

*.dmnd

tax_dump (directory)

Directory of the NCBI tax dump database

busco_lineages (string)

CSV list of odb's to run in blobtoolkit

taxon (integer)

Target organisms taxid

[0-9].*

btk_extra_opts (map)

Map of extra arguments for blobtoolkit

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 Blobtoolkit

versions_blobtoolkitgenerateparamsfile

${task.process} (string)

The name of the process

blobtoolkit_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

blobtoolkit_generateparamsfile (string)

The name of the tool

1.0.0 (string)

The expression to obtain the version of the tool

Tools

blobtoolkit_generateparamsfile Documentation

not a real tool!

doi: no DOI available
Authors