Description

Assess a genome FASTA with BUSCO using a chosen lineage and optional local lineage database path, then emit BUSCO gene coordinates as three bedGraph-style tables (Complete, Duplicated, Fragmented). Optionally bgzip/tabix those bedGraph files.

Input

Name
Description
Pattern

ch_fasta (file)

Input assembly FASTA (optionally gzipped). Structure: [ val(meta), path(fasta) ]

*.{fa,fsta,fna,fasta}{,.gz}

ch_busco_lineage (string)

BUSCO lineage dataset name (for example bacteria_odb10) aligned by meta with ch_fasta. Structure: [ val(meta), val(lineage_string) ]

val_busco_lineages_path (path)

Directory passed to BUSCO as --download_path (pre-downloaded lineages). Use an empty Groovy list [] to let BUSCO download datasets instead.

val_zip_bedgraph (boolean)

When true, run htslib/bgziptabix on each of the three bedGraph outputs ({prefix}.complete_buscos.bedgraph, {prefix}.duplicated_buscos.bedgraph, {prefix}.fragmented_buscos.bedgraph). When false, gz_index is an empty channel.

Output

Name
Description
Pattern

complete_bedgraph (file)

BUSCO Complete hits as tab-separated sequence, start, end, score ({prefix}.complete_buscos.bedgraph). Structure: [ val(meta), path(prefix.complete_buscos.bedgraph) ]

*.complete_buscos.bedgraph

duplicated_bedgraph (file)

BUSCO Duplicated hits ({prefix}.duplicated_buscos.bedgraph). Structure: [ val(meta), path(prefix.duplicated_buscos.bedgraph) ]

*.duplicated_buscos.bedgraph

fragmented_bedgraph (file)

BUSCO Fragmented hits ({prefix}.fragmented_buscos.bedgraph). Structure: [ val(meta), path(prefix.fragmented_buscos.bedgraph) ]

*.fragmented_buscos.bedgraph

full_table (file)

BUSCO full_table.tsv when BUSCO completes successfully.

full_table.tsv

busco_dir (directory)

BUSCO output directory tree for the sample.

batch_summary (file)

BUSCO batch_summary.txt derived output.

short_summaries_txt (file)

BUSCO short_summary *.txt files when produced.

short_summaries_json (file)

BUSCO short_summary *.json files when produced.

busco_log (file)

BUSCO run log when produced.

gz_index (file)

[ val(meta), path(*.gz), path(*.{tbi,csi}) ] per bgzip/tabixed bedGraph when val_zip_bedgraph is true; empty when false.

versions (file)

Mixed software version tuples from BUSCO and the converter process (versions topic).

versions.yml

Components

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