fasta_classify_catpack
Taxonomic classification of binned MAGs and contigs using CAT/BAT (CAT_pack).
Input
Channel containing binned MAG FASTA files.
Structure: [ val(meta), path(fasta) ]
*.{fa,fasta,fna} Channel containing contig FASTA files. Provide channel.empty() to skip
contig classification.
Structure: [ val(meta), path(fasta) ]
*.{fa,fasta,fna} Channel containing a pre-built CAT/BAT database. Can be a directory with db/ and tax/
subdirectories, or a .tar.gz archive of such a directory. Provide channel.empty() to
trigger automatic database download using ch_cat_db_download_id. Supplying both
ch_cat_db and ch_cat_db_download_id will cause a runtime error.
Structure: [ val(meta), path(db) ]
Channel containing the database identifier to download via CATPACK_DOWNLOAD (e.g. ‘nr’).
Only used when ch_cat_db is channel.empty(). Provide channel.empty() when supplying a
pre-built database via ch_cat_db. Supplying both inputs will cause a runtime error.
Structure: [ val(meta), val(db_id) ]
Whether to run CATPACK_SUMMARISE on the classification outputs. Requires
ext.args = “—only_official” to be set on CATPACK_ADDNAMES_BINS and
CATPACK_ADDNAMES_CONTIGS in the pipeline configuration, as CATPACK_SUMMARISE
requires official-rank headers in its input.
Output
Raw per-bin taxonomic classification file produced by CATPACK_BINS, before human-readable
names are added by CATPACK_ADDNAMES. Useful for downstream tools that consume the raw
CAT_pack output directly.
Structure: [ val(meta), path(txt) ]
*.bin2classification.txt Per-bin taxonomic classification with human-readable names added by CATPACK_ADDNAMES.
Structure: [ val(meta), path(txt) ]
*.txt Summary of bin classifications produced by CATPACK_SUMMARISE. Empty channel when
run_summarise is false.
Structure: [ val(meta), path(txt) ]
*.txt Raw per-contig taxonomic classification file produced by CATPACK_CONTIGS, before
human-readable names are added by CATPACK_ADDNAMES. Empty channel when ch_contigs
is channel.empty(). Useful for downstream tools that consume the raw CAT_pack output directly.
Structure: [ val(meta), path(txt) ]
*.contig2classification.txt Per-contig taxonomic classification with human-readable names added by CATPACK_ADDNAMES.
Empty channel when ch_contigs is channel.empty().
Structure: [ val(meta), path(txt) ]
*.txt Summary of contig classifications produced by CATPACK_SUMMARISE. Empty channel when
ch_contigs is channel.empty() or run_summarise is false.
Structure: [ val(meta), path(txt) ]
*.txt included in
included modules and subworkflows
maintainers
