bwamem2

Align paired-end DNA sequencing fastq files using bwa-mem2

usage

nexus run --nf-workflow alignment_bwamem2.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --abra2_targets_bed_file /path/to/file.bed \
    --known_sites_vcf_files "" \
    --chromosomes "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY,chrM" \
    --platform_tag "illumina" \
    --platform_unit_tag "unknown" \
    --library_tag "unknown"

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_1’, ‘fastq_file_2’.
--output_dir	Directory to which output files will be copied.
--reference_genome_fasta_file	Reference genome FASTA file.
--abra2_targets_bed_file	ABRA2 targets BED file.
--known_sites_vcf_files	GATK4 BaseRecalibrator –known-sites files. At least one VCF file must be supplied. Note that VCF files should be separated by commas.
--chromosomes	Chromosomes to recalibrate using GATK4 (default: ‘chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY,chrM’).
--platform_tag	Platform tag (default: ‘illumina’).
--platform_unit_tag	Platform unit tag (default: ‘unknown’).
--library_tag	Library tag (default: ‘unknown’).
--perform_local_indel_realignment	Perform local INDEL realignment (default: true).