sqanti3-fasta

Characterize isoforms using Sqanti3 (FASTA mode)

usage

nexus run --nf-workflow isoform_characterization_sqanti3-fasta.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --reference_genes_gtf_file /path/to/file.gtf \
    --params_sqanti3_qc "--aligner_choice minimap2 --report html --force_id_ignore" \
    --params_sqanti3_filter "ml"

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’, ‘fasta_file’.
--output_dir	Directory to which output files will be copied.
--reference_genome_fasta_file	Reference genome FASTA file.
--reference_genes_gtf_file	Reference genes GTF file.
--params_sqanti3_qc	sqanti3_qc.py parameters (default: ‘“–aligner_choice minimap2 –report html –force_id_ignore –isoAnnotLite”’). Note that the parameters need to be wrapped in quotes.
--params_sqanti3_filter	sqanti3_filter.py parameters (default: ‘“ml”’). Note that the parameters need to be wrapped in quotes.