bionic (1) slurm_srst2.1.gz

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.