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AMR prediction Pipeline version 1.0
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Mandatory arguments:
--input_dir Path to input dir. This must be used in conjunction with fastq_pattern
--fastq_pattern The regular expression that will match fastq files e.g '*_{1,2}.fastq.gz'
--output_dir Path to output dir
Optional ariba arguments:
--ariba_database_dir Path to a local dir containing ariba resitance database (default is ariba_databases/ncbi_db_2019-10-30.1)
--ariba_summary_arguments Supply the non-default options for the ariba summary command.
Wrap these in quotes e.g '--preset minimal --min_id 95'
(default is '--cluster_cols assembled,match,ref_seq,pct_id,ctg_cov')
--species If point-based mutations are required specify a species. This must be one of
campylobacter
enterococcus_faecalis
enterococcus_faecium
escherichia_coli
helicobacter_pylori
klebsiella
mycobacterium_tuberculosis
neisseria_gonorrhoeae
salmonella
staphylococcus_aureus
This pipeline will run ARIBA on two AMR prediction databases in parallel
Samples will be processed using a NCBI database of acquired AMR genes
Samples will be processed using the resfinder4 software and the predicted antimicrobial sensitivities found in the files full_summary.tsv and species_specific_summary.tsv in a sub-directory named resfinder within the output directory set using --output_dir
The test dataset can be run using this command
NXF_VER=19.11.0-edge nextflow run main.nf --input_dir $PWD/test_input --fastq_pattern '*{R,_}{1,2}.fastq.gz' --output_dir $PWD/test_output --depth_cutoff 100 --species staphylococcus_aureus -resume