wrangler

Synopsis

singularity run [run options...] --app wrangler <container> [app options...]

Description

Run MIPWrangler on demultiplexed data.

Options

# Required
-e    A unique ID given to each sequencing run by the user.
-l    File providing a list of samples with associated information.
-p    Probe sets to be processed.
-s    Sample sets to be processed.
-x    Additional arguments passed to MIPWrangler mipSetupAndExtractByArm,
      which extracts sequences and stitches paired end reads to single
      sequences.

# Optional
-c    Number of available processors to use.
-f    Population fraction cutoff used by MIPWrangler.
-h    Print the help page.
-k    Keep intermediate files generated by MIPWrangler.
-m    Minimum capture length for stitching excluding probe arms.
-n    Starting number for MIP server.
-o    Absolute path to MIPWrangler run script.
-t    The threshold at which UMIs will be downsampled. For any MIPs with more
      UMIs than this threshold, the number of UMIs will be reduced to the
      threshold.
-w    Whether to apply a weight when randomly sampling UMIs. UMIs are
      weighed by their read counts.

Defaults

# Required
-x    Default: 'none'

# Optional
-c    Default: 1
-f    Default: 0.005
-k    Default: false
-m    Default: 100
-n    Default: 1
-o    Default: '/opt/bin/runMIPWranglerCurrent.sh'
-t    Default: 2000
-w    Default: false

Examples

# Define variables
probe_sets='DR1,VAR4'
sample_sets='JJJ'
stitch_options='--stitchGapExtend=1,--overWriteDirs'

# Run app
singularity run \
  -B project_resources:/opt/project_resources \
  -B fastqs:/opt/data \
  -B wrangler_dir:/opt/analysis \
  --app wrangler miptools.sif \
  -e 'example' -l 'sample_list.tsv' -p ${probe_sets} \
  -s ${sample_sets} -x ${stitch_options}

singularity run \
  -B project_resources:/opt/project_resources \
  -B fastqs:/opt/data \
  -B wrangler_dir:/opt/analysis \
  --app wrangler miptools.sif \
  -c 10 -e 'example2' -l 'sample_list.tsv' -p ${probe_sets} \
  -s ${sample_sets} -x ${stitch_options} -k