NAME

       slurm_srst2 - running srst2 against multiple read sets

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]

DESCRIPTION

       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

AUTHOR

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.