diamond-blastp

Align peptide fasta files using Diamond Blastp

usage

nexus run --nf-workflow alignment_diamond-blastp.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --database_dmnd_file /path/to/file \
    --params_diamond_blastp ""

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.
--database_dmnd_file	Diamond-prepared local Blast database file.
--params_diamond_blastp	Diamond blastp parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes and a space at the end of the string is necessary.