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Supported File Formats

The EFSA Pipeline validation module supports various file formats for genomic data input.

Genome Files

Supported Input Formats Final Output Format
FASTA: .fasta, .fa, .fna .fasta
GenBank: .gb, .gbk, .genbank .fasta
Compression: .gz, .bz2, .gzip, .bzip2 Uncompressed

Details

  • GenBank files are automatically converted to FASTA format
  • Compressed files are decompressed during validation
  • Output is always uncompressed FASTA format

Read Files

Supported Input Formats Final Output Format
FASTQ: .fastq, .fq .fastq
BAM: .bam (limited support) .bam
Compression: .gz, .bz2, .gzip, .bzip2 .gz

Details

  • FASTQ files remain in FASTQ format
  • Compressed reads are kept compressed (using gzip)
  • BAM files have limited support and require special handling

Feature Files

Supported Input Formats Final Output Format
GFF: .gff, .gff3, .gtf .gff3
BED: .bed .gff3
Compression: .gz, .bz2, .gzip, .bzip2 Uncompressed

Details

  • All feature formats are converted to GFF3 via gffread
  • BED files are automatically converted to GFF3 format
  • Output is always uncompressed
  • If gffread fails or returns 0 features, the validator falls back to direct GFF3 parsing
  • If both gffread and the fallback parser return 0 features, validation fails: no output file is created and run_vcf_annotation is set to false in validated_params.json
  • Coordinate validation (start >= 1, start <= end) runs in strict mode; issues are reported as warnings

File Organization

Input files should be placed in: 

data/inputs/

After validation, files are organized in: 

data/valid/
├── assembled_genome.fasta
├── reference_genome.fasta
├── ref_plasmid.fa
├── mod_plasmid.fa
├── ref_feature.gff
├── illumina/
├── ont/
└── pacbio/

See Also