decontaminate_contigs
Description¶
MGnify decontamination workflow for contigs. Decontamination algorithm: Remove contigs with query coverage ≥ min_qcov AND percentage identity ≥ min_pid
Installation¶
ebi-metagenomics/decontaminate_contigs
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install decontaminate_contigs
Components¶
This subworkflow uses the following components:
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
contigs_and_reference |
tuple | An input channel containing one or more tuples with pairs contigs - contaminant reference. Fasta files can be compressed or uncompressed. Structure: [ [meta, assembly_fasta], reference_fasta ] | *.{fa,fna,fasta}[.gz] |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
cleaned_contigs |
map | Channel containing decontaminated assembly contigs. Structure: [ val(meta), path(fasta_file) ] | *.{fa,fna,fasta}[.gz] |
mapped_contigs_tsv |
map | Optional channel with a gzipped TSV listing the contaminated contigs, their query coverage and identity to the reference. Only emitted when at least one contig was flagged as contaminated. Structure: [ val(meta), path(tsv_gz_file) ] | *_mapped.tsv.gz |
mapped_contigs_tsv_mqc |
map | Optional channel with a gzipped copy of the contaminated contigs TSV carrying a MultiQC custom-content front-matter header, so MultiQC picks it up as a distinct table. Only emitted when at least one contig was flagged as contaminated. Structure: [ val(meta), path(tsv_gz_file) ] | *_mapped_mqc.tsv.gz |
versions |
file | File containing software versions. Structure: [ path(versions.yml) ] | versions.yml |
