NF-BINQC

aws batch submit-job \
    --job-name nf-binqc-1019-1 \
    --job-queue default-maf-pipelines \
    --job-definition nextflow-production \
    --container-overrides command=FischbachLab/nf-binqc,\
"--fastas","s3://nextflow-pipelines/nf-binqc/test/data"

aws batch submit-job \
    --job-name nf-binqc-SCv2_4_20210212 \
    --job-queue priority-maf-pipelines \
    --job-definition nextflow-production \
    --container-overrides command=FischbachLab/nf-binqc,\
"--fastas","s3://maf-versioned/ninjamap/Index/SCv2_4_20210212/fasta",\
"--project","SCv2_4_20210212"

or locally

nextflow run . --fastas test/data --project 00_TEST --outdir test/result/

Update

Note that updating the code here will not update the pipeline automatically.

cd nf-binqc
aws s3 sync . s3://nextflow-pipelines/nf-binqc --exclude ".git/*" --exclude "test/result/*" --delete --profile maf

MITI MCB strain QC example batch job

One step submission to generate report. No local post-processing needed any longer.

Input fasta files must be defined using either '--fastas' or '--seedfile' parameter.

Note that all assembled genome files are saved in one location and supplied to the --fastas option or supply a seedfile defining the genome name and s3 path in a csv file without headers. Below is an example seedfile.

SH0001342-00095,s3://genomics-workflow-core/Results/HybridAssembly/MITI-MCB/SH0001342-00095/UNICYCLER/assembly.fasta
SH0001372-00039,s3://genomics-workflow-core/Results/HybridAssembly/MITI-MCB/SH0001372-00039/UNICYCLER/assembly.fasta

The batch submission example using --fastas option

aws batch submit-job \
    --job-name nf-binqc-MCB \
    --job-queue priority-maf-pipelines \
    --job-definition nextflow-production \
    --container-overrides command="FischbachLab/nf-binqc, \
"--ext", "fasta", \
"--fastas","s3://genomics-workflow-core/Results/BinQC/MITI-MCB/20221018/fasta", \
"--project","20221018_207_v2", \
"--tree","true", \
"--outdir","s3://genomics-workflow-core/Results/BinQC/MITI-MCB" "

The batch submission example using --seedfile option

aws batch submit-job \
    --job-name nf-binqc-MCB \
    --job-queue priority-maf-pipelines \
    --job-definition nextflow-production \
    --container-overrides command="FischbachLab/nf-binqc, \
"--ext", "fasta", \
"--seedfile", "s3://genomics-workflow-core/Results/BinQC/TEST/20221018_207_v2.seedfile.csv"
"--project","20221018_207_v2", \
"--tree","true", \
"--outdir","s3://genomics-workflow-core/Results/BinQC/MITI-MCB" "

The structure of the output directory

00_Fasta/
01_SeqKit/
02_Barrnap/
03_CheckM/
04_GTDBtk/
05_REPORT/
06_GUNC/
07_TREE/ (optional)

Example: The QC report and pdf tree files are saved in the 05_REPORT and 06_TREE directories, respectively.

s3://genomics-workflow-core/Results/BinQC/MITI-MCB/20221018_207_v2/05_REPORT/20221018_207_v2.report.csv
s3://genomics-workflow-core/Results/BinQC/MITI-MCB/20221018_207_v2/06_TREE/20221018_207_v2.bestTree.pdf

Reference1: Generating the Whole Genome Trees

kSNP4.1 is a k-mer based SNP calling tool that can be used to generate whole genome trees.

Reference2: GUNC

GUNC is a Python package for Detection of chimerism and contamination in prokaryotic genomes. GUNC Documentation