Description

KRAKEN2 build custom database subworkflow

Input

Name (Type)
Description
Pattern

ch_fasta (file)

Channel containing a meta with a list of FASTAs to be built
Structure: [ val(meta), [ fasta1, fasta2, fasta3 ] ]

*.{fasta,fa,fna}

ch_taxonomy_names (file)

Channel containing a NCBI-style taxdump names file
Structure: [ names.dmp ]

names.dmp

ch_taxonomy_nodes (file)

Channel containing a NCBI-style taxdump nodes file
Structure: [ nodes.dmp ]

nodes.dmp

ch_accession2taxid (file)

Channel containing a NCBI-style taxdump accession2taxid (acc2tax) file
Structure: [ accession2taxid_file ]

*.accession2taxid

val_cleanintermediate (boolean)

Boolean flag whether to clean up intermediate files after build or not
Structure: [ val_cleanintermediate ]

true|false

Output

Name (Type)
Description
Pattern

db (directory)

Channel containing KRAKEN2 database directory files.
Use ext.prefix in a modules.conf file to change default name
Structure: [ val(meta), path(db) ]

*/

versions (file)

File containing software versions
Structure: [ path(versions.yml) ]

versions.yml
included modules and subworkflows
kraken2/add kraken2/build
maintainer
Github user jfy133
get in touch
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