isonform_clustered

Assemble clustered long-read RNA FASTQ files using isONform

usage

nexus run --nf-workflow assembly_isonform_clustered.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --params_isonform "--k 20 --w 31 --xmin 14 --xmax 80 --exact_instance_limit 50 --max_seqs_to_spoa 200 --delta_len 10 --delta_iso_len_3 30 --delta_iso_len_5 50 --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’, ‘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_isonform	isONform_parallel parameters (default: ‘“--k 20 --w 31 --xmin 14 --xmax 80 --exact_instance_limit 50 --max_seqs_to_spoa 200 --delta_len 10 --delta_iso_len_3 30 --delta_iso_len_5 50 --iso_abundance 3”’). Note that the parameters need to be wrapped in quotes. Do NOT pass --write_fastq; the batch script reads back transcriptome.fasta. --t, --fastq_folder, --outfolder, --tmpdir and --split_wrt_batches are set by the batch script and must not be overridden here.