rattle_clustered

Assemble clustered long-read RNA FASTQ files using RATTLE

usage

nexus run --nf-workflow assembly_rattle_clustered.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --params_rattle_cluster "--iso --rna" \
    --params_rattle_correct "" \
    --params_rattle_polish "--rna"

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’, ‘tsv_file’ (columns: ‘cluster_id’, ‘read_name’), ‘cluster_method’ (name of the tool that produced tsv_file, e.g. ‘isonclust3’; keeps repeat clusterings of one sample apart).
--output_dir	Directory to which output files will be copied.
--params_rattle_cluster	RATTLE cluster parameters (default: ‘“--iso --rna”’). Note that the parameters need to be wrapped in quotes.
--params_rattle_correct	RATTLE correct parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.
--params_rattle_polish	RATTLE polish parameters (default: ‘“--rna”’). Note that the parameters need to be wrapped in quotes. --input, --clusters, --output, --output-folder, -t and --summary are set by the batch script; do not pass them here.