de-souza

Identify RNA variants in long-read RNA sequencing FASTQ files using lrRNAseqVariantCalling (de Souza et al., Genome Biology 2023)

usage

nexus run --nf-workflow variant_calling_de-souza.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --deepvariant_input_path /path/to/dir/ \
    --deepvariant_output_path /path/to/dir/ \
    --params_minimap2 "-ax splice -uf -C5 --secondary=no" \
    --params_samtools_view "-F 2308" \
    --platform_tag "unknown" \
    --platform_unit_tag "unknown" \
    --library_tag "unknown" \
    --deepvariant_containerization "singularity" \
    --deepvariant_model_type "PACBIO" \
    --deepvariant_bin_path "/opt/deepvariant/bin/run_deepvariant" \
    --deepvariant_bin_version "1.6.1"

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.
--reference_genome_fasta_file	Reference genome FASTA file.
--deepvariant_input_path	DeepVariant input path.
--deepvariant_output_path	DeepVariant output path.
--params_minimap2	Minimap2 parameters (default: ‘“-ax splice -uf -C5 –secondary=no”’). Note that the parameters need to be wrapped in quotes.
--params_samtools_view	Samtools view parameters (default: ‘“-F 2308”’). Note that the parameters need to be wrapped in quotes.
--platform_tag	Platform tag (default: ‘unknown’).
--platform_unit_tag	Platform unit tag (default: ‘unknown’).
--library_tag	Library tag (default: ‘unknown’).
--deepvariant_containerization	DeepVariant containerization (‘singularity’ or ‘docker’; default: ‘singularity’).
--deepvariant_model_type	DeepVariant –model_type parameter value (default: ‘PACBIO’).
--deepvariant_bin_path	DeepVariant bin path (default: ‘/opt/deepvariant/bin/run_deepvariant’).
--deepvariant_bin_version	DeepVariant bin version (default: ‘1.6.0’).