fasta_build_add_kraken2

KRAKEN2 build custom database subworkflow

metagenomicskraken2databasebuildcustom

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/fasta_build_add_kraken2

Description

KRAKEN2 build custom database subworkflow

Input

name

description

pattern

`ch_fasta`

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

*.{fasta,fa,fna}

`ch_taxonomy_names`

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

names.dmp

`ch_taxonomy_nodes`

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

nodes.dmp

`ch_accession2taxid`

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

*.accession2taxid

`val_cleanintermediate`

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

true|false

`ch_custom_seqid2taxid`

Optional custom or prebuilt seqid2taxid text file. If not provided, it will be generated by kraken2-build.

seqid2taxid.map

Output

name

description

pattern

`db`

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

kraken2-database/

`db_separated`

Channel containing a list of KRAKEN2 database directory files as separate elements of a tuple.
Use publishDir in a modules.conf file to change default name for user
Structure: [ val(meta), path(k2d_files), path(map_files), path(added_files), path(taxonomy_files) ]