Overview

This document provides a walkthrough of executing the AMRScan workflow using Nextflow DSL2. The pipeline identifies antimicrobial resistance (AMR) genes using BLAST against the CARD database.

Command Execution

We launch the workflow using the following command:

nextflow run workflow/AMRScan.nf \
    --input data/*.fna \
    --outdir results \
    --evalue 1e-10 \
    --threads 8 \
    --min_quality 25

System Output

 N E X T F L O W   ~  version 25.04.6

Launching `workflow/AMRScan.nf` [mad_monod] DSL2 - revision: ebe2e1ab36

==============================================
AMRScan - Antimicrobial Resistance Scanner
==============================================
Input file        : data/GCF_037966445.1_ASM3796644v1_genomic.fna
Output directory  : results
CARD database     : db_demo/protein_fasta_protein_homolog_model.fasta
E-value threshold : 1e-10
Threads           : 8
Min quality       : 25
==============================================

executor >  local (4)
[e1/555c15] PREPROCESS_READS (GCF_037966445.1_ASM3796644v1_genomic) [100%] 1 of 1 ✔
[skipped  ] MAKEBLASTDB (CARD_database)                             [100%] 1 of 1, stored: 1 ✔
[55/2e8e1a] BLAST_SEARCH (GCF_037966445.1_ASM3796644v1_genomic)     [100%] 1 of 1 ✔
[65/da8049] PARSE_RESULTS (GCF_037966445.1_ASM3796644v1_genomic)    [100%] 1 of 1 ✔

==============================================
AMRScan workflow completed!
==============================================
Results directory: results
Success: true
Duration: 17s
==============================================

Results

summary_file <- "results/final/GCF_037966445.1_ASM3796644v1_genomic_AMR_hits_summary.csv"
if (file.exists(summary_file)) {
  amr_summary <- read.csv(summary_file)
  knitr::kable(head(amr_summary), caption = "Top AMR Hits Summary")
} else {
  cat("Summary file not found.")
}
Top AMR Hits Summary
Query Subject Identity Length Evalue Bitscore Annotation
NZ_JBBPBW010000028.1 gb|BAM10414.1|ARO:3003039|OprA 40.839 453 0 252 gb|BAM10414.1|ARO:3003039|OprA [Pseudomonas aeruginosa]
NZ_JBBPBW010000035.1 gb|ABV89601.1|ARO:3004826|LAP-2 100.000 285 0 587 gb|ABV89601.1|ARO:3004826|LAP-2 [Enterobacter cloacae]
NZ_JBBPBW010000001.1 gb|CAA66729.1|ARO:3001070|SHV-11 100.000 286 0 581 gb|CAA66729.1|ARO:3001070|SHV-11 [Klebsiella pneumoniae]
NZ_JBBPBW010000010.1 gb|CCI79240.1|ARO:3005047|eptB 99.303 574 0 1109 gb|CCI79240.1|ARO:3005047|eptB [Klebsiella pneumoniae subsp. rhinoscleromatis SB3432]
NZ_JBBPBW010000104.1 gb|AHK10285.1|ARO:3002859|dfrA14 98.726 157 0 327 gb|AHK10285.1|ARO:3002859|dfrA14 [Escherichia coli]
NZ_JBBPBW010000011.1 gb|AAC75271.1|ARO:3003952|YojI 83.912 547 0 885 gb|AAC75271.1|ARO:3003952|YojI [Escherichia coli str. K-12 substr. MG1655]

Notes