fasta_build_add_kraken2_bracken

KRAKEN2 and BRACKEN build custom database subworkflow

metagenomicskraken2databasebuildcustombracken

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/fasta_build_add_kraken2_bracken

Description

KRAKEN2 and BRACKEN 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_cleanintermediates :boolean`

Boolean flag whether to clean up intermediate files after build or not.
If val_runbrackenbuild set, will be ignored as BRACKEN requires intermediate files.
Structure: [ val_cleanintermediate ]

true|false

`val_runbrackenbuild :boolean`

Boolean flag whether to additionally insert required BRACKEN database files into KRAKEN2 directory.
Note any changes for k-mer or read lengths must come via Nextflow config ext.args.
Structure: [ val_runbrackenbuild ]

true|false

Output

name:type

description

pattern

`db :directory`

Channel containing KRAKEN2 (and BRACKEN) 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