Input Format

The repeat pipeline uses a CSV file to specify the genomes to analyse and the metadata required to retrieve repeat libraries and annotate repetitive elements.

CSV File Structure

Basic Format

The CSV file must contain a header row followed by one row per genome.

column1,column2,column3
value1,value2,value3
value1,value2,value3

!!! important “CSV Requirements”

Header row required: The first row must contain column names.
Comma-separated: Use commas as delimiters.
One genome per row: Each row represents a single assembly.
No trailing spaces: Remove leading and trailing whitespace from all values.

Required Columns

The repeat pipeline requires the following information for each genome.

Column	Type	Required	Description	Example
`gca`	string	✅	NCBI assembly accession	`GCA_000001405.29`
`taxon_id`	integer	✅	NCBI taxonomy identifier	`9606`
`repeatmodeler_library`	string	⚠️ Optional	path to a RepeatModeler repeat library	`repeatmodeler.fa`

If no RepeatModeler library is supplied, the pipeline can fall back to the configured repeat annotation strategy (for example Dfam or de novo repeat discovery, depending on the selected parameters).

Example CSV

gca,taxon_id,repeatmodeler_library
GCA_000001405.29,9606,https://ftp.ensembl.org/pub/repeats/homo_sapiens.repeatmodeler.fa
GCA_000001635.9,10090,https://ftp.ensembl.org/pub/repeats/mus_musculus.repeatmodeler.fa
GCA_000002035.4,7955,

Typical Command

nextflow run main.nf \
  --csvFile genomes.csv \
  --run_repeatmasker \
  --run_red

Column Details

`gca`

NCBI GenBank genome assembly accession.

Format:

GCA_000000000.0

Examples:

GCA_000001405.29
GCA_000001635.9
GCA_000002035.4

Assemblies are downloaded automatically from NCBI when required.

`taxon_id`

NCBI Taxonomy identifier.

Examples:

Species	Taxonomy ID
Homo sapiens	9606
Mus musculus	10090
Danio rerio	7955
Drosophila melanogaster	7227

Taxonomy identifiers are used to select appropriate repeat resources when available.

`repeatmodeler_library`

Optional path pointing to a RepeatModeler repeat library.

Example:

path/homo_sapiens.repeatmodeler.fa

If omitted, the pipeline uses the configured fallback strategy.

Complete Example

gca,taxon_id,repeatmodeler_library
GCA_000001405.29,9606,path/homo_sapiens.repeatmodeler.fa
GCA_000001635.9,10090,path/mus_musculus.repeatmodeler.fa
GCA_000002035.4,7955,

Command:

nextflow run main.nf \
    --csvFile genomes.csv \
    --run_repeatmasker \
    --run_red \
    --outdir results

Validation

The input CSV is validated before the pipeline starts.

Typical validation errors include:

❌ Invalid GCA accession

Error: GCA must follow the format GCA_000000000.0

❌ Missing taxonomy identifier

Error: taxon_id is required

❌ Invalid RepeatModeler path

Error: RepeatMasker library not specified

The CHECK_AND_DOWNLOAD_RMLIBRARY process validates remote URLs before the workflow continues.

Tips and Best Practices

!!! tip “Use public RepeatModeler libraries”

Whenever possible, provide curated RepeatModeler libraries generated for the target assembly.

!!! tip “Verify URLs”

Ensure URLs are accessible before launching the pipeline.

wget --spider https://your.server/repeatmodeler.fa

!!! tip “Use stable GCA accessions”

Always use the final assembly accession rather than intermediate versions.

!!! tip “Run RED together with RepeatMasker”

Using both methods provides complementary repeat annotations.

Schema Validation

The CSV file is validated against the repeat pipeline input schema.

cat pipelines/repeat/assets/schema_input.json

You can also validate the inputs by running:

nextflow run main.nf --csvFile genomes.csv --help