nf-core/phageannotator

Path to comma-separated file containing information about the samples in the experiment.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Email address for completion summary.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Minimum assembly length

Run ViromeQC to estimate viral enrichment

Run MASH screen to identify external viruses contained in reads

Path to FASTA file containing reference virus sequences

Path to mash sketch file for reference virus sequences

Save reference virus sketch, if it was created.

Minimum mash screen score to consider a genome contained

Hashes present in multiple references are assigned only to top sequence

Skip running geNomad to classify viral/non-viral sequences

Path to directory containing geNomad’s database

Save geNomad’s database, if it was downloaded.

Minimum virus score for a sequence to be considered viral

Maximum FDR for a sequence to be considered viral (will include —enable-score-calibration)

Number of splits for running geNomad (more splits lowers memory requirements)

Run COBRA to extend viral contigs

The assembler that was used to assemble viral contigs

Minimum kmer value used during assembly

Maximum kmer value used during assembly

Skip running CheckV to assess virus quality and filter sequences

Path to directory containing CheckV database

Save CheckV’s database, if it was downloaded

Minimum virus length to pass filtering

Minimum CheckV completeness to pass filtering

Remove viruses labeled as provirus by geNomad or CheckV

Remove viruses with CheckV warnings

Skip ANI-based virus clustering

Minimum precent identity for BLAST hits

Maximum number of BLAST hits to record for each sequence

Minimum average nucleotide identity (ANI) for sequences to be clustered together

Minimum query coverage for sequences to be clustered together

Minimum test coverage for sequences to be clustered together

Skip read alignment to viral sequences

Minimum length of reads aligned to references

Minimum percent identity of aligned reads

Minimum percent of read aligned to references

Abundance calculation metrics

Run iPHoP to predict phage hosts

Path to locally iPHoP database

Save downloaded iPHoP database

Minimum confidence score to provide host prediction

Run BACPHLIP to predict virus lifestyle

Run pharokka to predict and annotate phage ORFs

Path to predownloaded pharokka db

Bypass microdiversity analysis with inStrain

Minimum identity for read alignment to be considered

Minimum MAPQ for a read to be considered

Minimum coverage for a variant to be considered

Minimum allele frequency for an SNP to be considered

Maximum FDR for a SNP to be considered

Minimum number of reads mapping to a genome to consider profiling

Minimum identity for genomes to be considered in the same strain

Minimum percent of genomes compared for comparison to be considered

Minimum breadth of coverage for a genome to be considered present

Custom MultiQC yaml file containing HTML including a methods description.

Use logo in initialise subworkflow