isonform

Assemble long-read RNA FASTQ files using isONform

usage

nexus run --nf-workflow assembly_isonform.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --params_ison_pipeline "--mode pacbio --iso_abundance 3"

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_ison_pipeline	isON_pipeline.sh parameters (default: ‘“--mode pacbio --iso_abundance 3”’). Note that the parameters need to be wrapped in quotes.