isugifNF/blast
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isugifNF/blast v1.0.0
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Introduction
isugifNF/blast is a nextflow pipeline for BLAST-ing a fasta sequence file against a genome.
The workflow processes many sequences from a large fasta file --query, splits them into smaller fasta files, and parallel BLAST them against a given genome --genome. The pipeline can be run on a local laptop -profile local or on an HPCC cluster -profile ceres or -profile condo.
Installation and running on Ceres HPCC
Nextflow is already installed on Ceres HPCC. Therefore, running isugifNF/blast involves (1) allocating a debug node salloc -N 1 -p debug -t 01:00:00, (2) loading nextflow module load nextflow, and (3) running the pipeline nextflow run isugifNF/blast. The --help flag prints out the usage statement.
salloc -N 1 -p debug -t 01:00:00
module load nextflow
nextflow run isugifNF/blast --helpsee usage statement
``` Usage: The typical command for running the pipeline is as follows: nextflow run parallelBLAST.nf --query QUERY.fasta --genome GENOME.fasta -profile local nextflow run parallelBLAST.nf --query QUERY.fasta --dbDir "blastDatabaseDirectory" --dbName "blastPrefixName" -profile local Mandatory arguments: --query Query fasta file of sequences you wish to BLAST --genome Genome from which BLAST databases will be generated or --query Query fasta file of sequences you wish to BLAST --dbDir BLAST database directory (full path required) --dbName Prefix name of the BLAST database -profile Configuration profile to use. Can use multiple (comma separated) Available: test, condo, ceres, local, nova Optional arguments: --outdir Output directory to place final BLAST output --outfmt Output format ['6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen frames salltitles qcovs'] --options Additional options for BLAST command [-evalue 1e-3] --outfileName Prefix name for BLAST output [blastout] --threads Number of CPUs to use during blast job [16] --chunkSize Number of fasta records to use when splitting the query fasta file --app BLAST program to use [blastn;blastp,tblastx,blastx] --help This usage statement. ```Dependencies if running locally
Nextflow is written in groovy which requires java version 1.8 or greater (check version using java -version). But otherwise can be installed if you have a working linux command-line.
java -version
curl -s https://get.nextflow.io | bash
# Check to see if nextflow is created
ls -ltr nextflow
#> total 32
#> -rwx--x--x 1 username staff 15K Aug 12 12:47 nextflowThe pipeline isugifNF/blast can be run using singularity/docker containers or with a local install of BLAST. For a local install, select the appropriate installer if you are on windows (*.exe), linux (*linux.tar.gz), or MacOS (*.dmg). There are a few different ways to install BLAST locally, including brew, ports, and conda.
# test run using locally installed blast
nextflow run isugifNF/blast -profile test
# test run using containers (docker/singularity)
nextflow run isugifNF/blast -profile test,docker
nextflow run isugifNF/blast -profile test,singularity
# test run on Ceres HPC
nextflow run isugifNF/blast -profile test,ceresDocker/singularity runs will take a few minutes since it needs to download the ncbi/blast container. Subsequent runs will be faster.
Credits
These scripts were originally written for use on Ceres and Condo HPCC by Andrew Severin (@isugif), Siva Chudalayandi (@Sivanandan), and Jennifer Chang (@j23414)