isugifNF/blast

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      isugifNF/blast  v1.0.0       
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Genome Informatics Facility |

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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 --help

see 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 nextflow

The 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,ceres

Docker/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)