fastq2unalignedbam

Convert FASTQ to unaligned BAM files using Picard

usage

nexus run --nf-workflow utilities_fastq2unalignedbam.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --read_type "single-end" \
    --params_picard ""

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.
--read_type	read type (default: ‘single-end’). Either ‘single-end’ or ‘paired-end’.
--params_picard	Picard ‘FastqToSam’ parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.