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