blastp

Align peptide fasta files using Blastp

usage

nexus run --nf-workflow alignment_blastp.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --blastdb_dir /path/to/dir/ \
    --blastdb_name "nr" \
    --params_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.
--blastdb_dir	Local Blast database path. The database can be downloaded by the following command: update_blastdb.pl –source gcp –decompress nr –num_threads 16
--blastdb_name	Local Blast database name (default: ‘nr’).
--params_blastp	Blastp parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes and a space at the end of the string is necessary.