rnabloom2

Assemble long-read RNA FASTQ files using RNA-Bloom2

usage

nexus run --nf-workflow assembly_rnabloom2.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --params_rnabloom2 "--qual 20 --qual-avg 20 --mincov 3 -ntcard -savebf -chimera -lrpb"

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’.
--output_dir	Directory to which output files will be copied.
--params_rnabloom2	RNA-Bloom2 parameters (default: ‘“–qual 20 –qual-avg 20 –mincov 3 -ntcard -savebf -chimera -lrpb”’). Note that the parameters need to be wrapped in quotes.