minimap2

Align long-read (DNA or RNA) fastq files using Minimap2

usage

nexus run --nf-workflow alignment_minimap2.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --params_minimap2 "-ax map-hifi --cs --eqx -Y -L --secondary=no" \
    --platform_tag "unknown" \
    --platform_unit_tag "unknown" \
    --library_tag "unknown"

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

parameter	description
--samples_tsv_file	TSV file with the following columns: ‘sample_id’, ‘fastq_file’. Multiple rows may share the same sample_id with different fastq_file values; all such fastq files are aligned together into a single merged BAM per sample_id (e.g., for combining haplotype A and haplotype B reads of the same sample).
--output_dir	Directory to which output files will be copied.
--reference_genome_fasta_file	Reference genome FASTA file.
--params_minimap2	Minimap2 parameters (default: “-ax map-hifi --cs --eqx -Y -L --secondary=no”). Note that the parameters need to be wrapped in quotes and a space at the end of the string is necessary.
--platform_tag	Platform tag (default: ‘unknown’).
--platform_unit_tag	Platform unit tag (default: ‘unknown’).
--library_tag	Library tag (default: ‘unknown’).