Running AMRFinderPlus for MDU
Project description
abriTAMR
abriTAMR is an AMR gene detection pipeline that runs AMRFinderPlus on a list of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.
Command-line tool
abritamr
:
abritamr --help
usage: abritamr [-h] [--mduqc] [--qc QC] [--positive_control POSITIVE_CONTROL]
[--Singularity] [--singularity_path SINGULARITY_PATH]
[--contigs CONTIGS] [--amrfinder_output AMRFINDER_OUTPUT]
[--workdir WORKDIR] [--resources RESOURCES]
[--drug_classes DRUG_CLASSES] [--jobs JOBS] [--keep]
MDU AMR gene detection pipeline
optional arguments:
-h, --help show this help message and exit
--mduqc, -m Set if running on MDU QC data. If set please provide
the MDU QC .csv as further input and an additional
output suitable for lims input will be provided.
(default: False)
--qc QC, -q QC Name of checked MDU QC file. (default:
mdu_qc_checked.csv)
--positive_control POSITIVE_CONTROL, -p POSITIVE_CONTROL
Path to positive control sequence - must be set if
using -m (default: )
--Singularity, -S If using singularity container for AMRfinderplus
(default: False)
--singularity_path SINGULARITY_PATH, -s SINGULARITY_PATH
Path to the singularity container for AMRfinderplus,
if empty will defualt to shub://phgenomics-
singularity/amrfinderplus (default: )
--contigs CONTIGS, -c CONTIGS
Tab-delimited file with sample ID as column 1 and path
to assemblies as column 2 (default: )
--amrfinder_output AMRFINDER_OUTPUT, -o AMRFINDER_OUTPUT
Tab-delimited file with sample ID as column 1 and path
to amr_finder output files as column 2 (default: )
--workdir WORKDIR, -w WORKDIR
Working directory, default is current directory
(default: /home/khhor/MDU/JOBS/ad_hoc/abritamr_in_para
llel/20191206)
--resources RESOURCES, -r RESOURCES
Directory where templates are stored (default: /home/k
hhor/miniconda3/envs/abritamr/lib/python3.7/site-
packages/abritamr)
--drug_classes DRUG_CLASSES, -d DRUG_CLASSES
Path to file (default: /home/khhor/miniconda3/envs/abr
itamr/lib/python3.7/site-
packages/abritamr/db/refgenes.csv)
--jobs JOBS, -j JOBS Number of AMR finder jobs to run in parallel.
(default: 16)
--keep, -k If you would like to keep intermediate files and
snakemake log. Default is to remove (default: False)
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