NF-BLAST

A Nextflow script that will run BLAST and using fasta files on S3 and databases available on a shared filesystem (EFS).

aws batch submit-job \
    --job-name nf-blast-SH0002532-00280 \
    --job-queue priority-maf-pipelines \
    --job-definition nextflow-production \
    --container-overrides command=fischbachlab/nf-blast,\
"--query","s3://genomics-workflow-core/Results/HybridAssembly/MITI-MCB/SH0002532-00280/20230505/UNICYCLER/assembly.fasta",\
"--project","MITI-MCB",\
"--sample_name","SH0002532-00280",\
"--db","immeDB",\
"--prefix","20230822"

Sample Parameters for Nextflow Tower

{
    "blast_type": "blastn",
    "db": "nt",
    "chunksize": 1000,
    "dbsize": 1000000,
    "outfmt": "'7 std qlen slen qcovs sscinames'",
    "max_aln": 500,
    "project": "00_Test",
    "prefix": "output-0929",
    "query": "s3://nextflow-pipelines/blast/data/TY0000004.cons.fa"
}

Example: Protein BLAST against CDD

aws batch submit-job \
    --job-name nf-blast-aap-cdd-4 \
    --job-queue priority-maf-pipelines \
    --job-definition nextflow-production \
    --container-overrides command=fischbachlab/nf-blast,\
"-r","sj-seedfile",\
"--seedfile","s3://genomics-workflow-core/Results/Blast/s_epi/aap/00_seedfiles/aap.seedfile.csv",\
"--blast_type","blastp",\
"--db","cdd",\
"--max_aln","5000",\
"--project","s_epi",\
"--prefix","aap"

Available databases

• nt- [Last Updated: 2023-12-05] version: 2023-12-02-01-05-02
• nr - [Last Updated: 2023-12-05] version: 2023-12-02-01-05-02
• ncbi_16s - [Last Updated: 2023-12-05] version: 2023-12-02-01-05-02
• silva SSU v138.1 - [Last Updated: 2021-07-22]
• silva_nr SSU v138.1 - [Last Updated: 2021-07-22]
• immeDB - [Last Updated: 2023-06-27]

By default

• the output is in the customized tabular format '7 std qlen slen qcovs', where 3 non-standard columns have been added.
• e-values are calculated based on a dbsize of 1e6, to allow comparison between results from different databases.
• a maximum of 500 alignments are allowed per query.
• the query file is split into smaller chunnks of 1000 sequences each, before running a blast on each chunk in parallel and finally merging into a single output table.

Using a seedfile to run Blast on multiple fasta files [PREFERRED]

Create a comma-separated seedfile, where first column is the sample name and second is the path to the fasta file. For example:

sample_name,fasta_file
SH0001852-00262,s3://genomics-workflow-core/Results/HybridAssembly/MITI-MCB/SH0001852-00262/20230120/UNICYCLER/assembly.fasta
SH0001328-00301,s3://genomics-workflow-core/Results/HybridAssembly/MITI-MCB/SH0001328-00301/20230610/UNICYCLER/assembly.fasta
SH0001374-00303,s3://genomics-workflow-core/Results/HybridAssembly/MITI-MCB/SH0001374-00303/20230602/UNICYCLER/assembly.fasta
SH0001378-00273,s3://genomics-workflow-core/Results/HybridAssembly/MITI-MCB/SH0001378-00273/20230602/UNICYCLER/assembly.fasta
SH0001421-00003,s3://genomics-workflow-core/Results/HybridAssembly/MITI-MCB/SH0001421-00003/20230602/UNICYCLER/assembly.fasta
SH0001515-00040,s3://genomics-workflow-core/Results/HybridAssembly/MITI-MCB/SH0001515-00040/UNICYCLER/assembly.fasta

Upload this file to the expected output location.

s3://genomics-workflow-core/Results/Blast/<PROJECT>/<PREFIX>/00_seedfile/seedfile.csv

Example:

s3://genomics-workflow-core/Results/Blast/MITI-MCB/20231106/00_seedfile/20231106_seedfile.csv

aws batch submit-job \
    --job-name nf-blast-seedfile-2 \
    --job-queue priority-maf-pipelines \
    --job-definition nextflow-production \
    --container-overrides command=fischbachlab/nf-blast,\
"--seedfile","s3://genomics-workflow-core/Results/AMRFinderPlus/MITI-MCB/20231106/00_seedfile/20231106_seedfile.csv",\
"--db","immeDB",\
"--project","MITI-MCB",\
"--prefix","20231106"

Where: 20231106 is today's date in the format YYYYMMDD.

Blast Databases

Available NCBI Databases

To see which NCBI databases are available to download and when they were last updated, run the following command:

docker run --rm \
  -w /blast/blastdb \
  ncbi/blast \
  update_blastdb.pl --showall pretty

Using the -params-file option

aws batch submit-job \
    --job-name nf-blast-aap-nr-limit-s-epi \
    --job-queue priority-maf-pipelines \
    --job-definition nextflow-production \
    --container-overrides command=fischbachlab/nf-blast,\
"-params-file","s3://genomics-workflow-core/Results/Blast/s_epi/aap/00_seedfiles/aap.s-epi.taxonId1282.json"