slurm_srst21

Options

slurm_srst2 [-h] [--walltime WALLTIME] [--memory MEMORY] [--rundir RUNDIR] --script SCRIPT --output OUTPUT [--input_se INPUT_SE [INPUT_SE ...]] [--input_pe INPUT_PE [INPUT_PE ...]] [--forward FORWARD] [--reverse REVERSE] [--other_args OTHER_ARGS]

Overview

Submit SRST2 jobs through SLURM (see srst(1))

Options

-h, --help

show this help message and exit

--walltime WALLTIME

wall time (default 0-1:0 = 1 h)

--memory MEMORY

mem (default 4096 = 4gb)

--rundir RUNDIR

directory to run in (default current dir)

--script SCRIPT

path to srst2 (default srst2)

--output OUTPUT

identifier for outputs (will be combined with read set identifiers)

--input_se INPUT_SE [INPUT_SE ...]

Single end read file(s) for analysing (may be gzipped)

--input_pe INPUT_PE [INPUT_PE ...]

Paired end read files for analysing (may be gzipped)

--forward FORWARD

Designator for forward reads (only used if NOT in MiSeq format sample_S1_L001_R1_001.fastq.gz; otherwise default is _1, i.e. expect forward reads as sample_1.fastq.gz)

--reverse REVERSE

Designator for reverse reads (only used if NOT in MiSeq format sample_S1_L001_R2_001.fastq.gz; otherwise default is _2, i.e. expect forward reads as sample_2.fastq.gz)

--other_args OTHER_ARGS

string containing all other arguments to pass to srst2