decontaminate_assemblies
Description¶
MGnify Production assembly decontamination subworkflow. Performs sequential decontamination of assembled contigs against the human genome, PhiX and a genome specified by the user (usually the sample host). It designed to remove any contigs that come from any of those references.
Installation¶
ebi-metagenomics/decontaminate_assemblies
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install decontaminate_assemblies
Components¶
This subworkflow uses the following components:
decontaminate_contigs(subworkflow)
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information and decontamination parameters. Expected keys: - phix_reference: Filename prefix of PhiX reference genome (optional, null to skip) - human_reference: Filename prefix of human reference genome (optional, null to skip) - contaminant_reference: Filename prefix of custom contaminant reference (optional, null to skip) | - |
assembly |
file | Assembly FASTA file containing contigs to be decontaminated | *.{fasta,fa,fna} |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information | - |
cleaned_contigs |
file | Decontaminated assembly FASTA file | *.{fasta,fa,fna} |
phix_contaminated_contigs_tsv |
file | Optional gzipped TSV listing contigs flagged as PhiX contamination, with their query coverage and identity to the PhiX reference. Only emitted when at least one contig was flagged. | *_mapped.tsv.gz |
human_contaminated_contigs_tsv |
file | Optional gzipped TSV listing contigs flagged as human contamination, with their query coverage and identity to the human reference. Only emitted when at least one contig was flagged. | *_mapped.tsv.gz |
host_contaminated_contigs_tsv |
file | Optional gzipped TSV listing contigs flagged as host/custom contaminant contamination, with their query coverage and identity to the reference. Only emitted when at least one contig was flagged. | *_mapped.tsv.gz |
phix_contaminated_contigs_tsv_mqc |
file | Optional gzipped copy of the PhiX 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. | *_mapped_mqc.tsv.gz |
human_contaminated_contigs_tsv_mqc |
file | Optional gzipped copy of the human 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. | *_mapped_mqc.tsv.gz |
host_contaminated_contigs_tsv_mqc |
file | Optional gzipped copy of the host/custom contaminant 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. | *_mapped_mqc.tsv.gz |
versions |
file | File containing software versions | versions.yml |
