bookend

Assemble long-read RNA FASTQ files using Bookend

usage

nexus run --nf-workflow assembly_bookend.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --params_bookend_assemble "" \
    --params_bookend_fasta ""

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’, ‘bam_file’, ‘bam_bai_file’.
--output_dir	Directory to which output files will be copied.
--reference_genome_fasta_file	Reference genome FASTA file.
--params_bookend_assemble	bookend assemble parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.
--params_bookend_fasta	bookend fasta parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.