nanoporeRunSVAnalysis

nanoporeRunSVAnalysis, workflow that generates structural variant files from input of nanopore fastq files, a wrapper of the workflow https://github.com/mike-molnar/nanopore-SV-analysis

Overview

Dependencies

Usage

Cromwell

java -jar cromwell.jar run nanoporeRunSVAnalysis.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
`sample`	String	name of all samples
`normal`	String	name of the normal samples
`tumor`	String	name of the tumor samples
`samplefile`	File	sample file
`runSVAnalysis.modules`	String	Names and versions of modules

Optional workflow parameters:

Parameter	Value	Default	Description

Optional task parameters:

Parameter	Value	Default	Description
`generateConfig.jobMemory`	Int	8	memory allocated for Job
`generateConfig.timeout`	Int	24	Timeout in hours, needed to override imposed limits
`runSVAnalysis.jobMemory`	Int	8	memory allocated for Job
`runSVAnalysis.timeout`	Int	24	Timeout in hours, needed to override imposed limits

Outputs

Output	Type	Description	Labels
`insertions`	File	output from rule run_SV_analysis of the original workflow	vidarr_label: insertions
`deletions`	File	output from rule run_SV_analysis of the original workflow	vidarr_label: deletions
`duplications`	File	output from rule run_SV_analysis of the original workflow	vidarr_label: duplications
`inversions`	File	output from rule run_SV_analysis of the original workflow	vidarr_label: inversions
`translocations`	File	output from rule run_SV_analysis of the original workflow	vidarr_label: translocations
`CNVs`	File	output from rule run_SV_analysis of the original workflow	vidarr_label: CNVs

Commands

This section lists command(s) run by nanoporerunsvanalysis workflow

Running nanoporerunsvanalysis

Configure

 set -euo pipefail
 cat <<EOT >> config.yaml
 workflow_dir: "/.mounts/labs/gsi/modulator/sw/Ubuntu18.04/nanopore-sv-analysis-20220505"
 conda_dir: "/.mounts/labs/gsi/modulator/sw/Ubuntu18.04/nanopore-sv-analysis-20220505/bin"
 reference_dir: "/.mounts/labs/gsi/modulator/sw/data/hg38-nanopore-sv-reference-20220505"
 samples: [~{sample}]
 normals: [~{normal}]
 tumors: [~{tumor}]
 ~{sample}: ~{samplefile}
 EOT

Run analysis as a Snakemake process

 module load nanopore-sv-analysis
 unset LD_LIBRARY_PATH
 set -euo pipefail
 cp $NANOPORE_SV_ANALYSIS_ROOT/Snakefile .
 cp ~{config} .
 $NANOPORE_SV_ANALYSIS_ROOT/bin/snakemake --jobs 16 --rerun-incomplete --keep-going --latency-wait 60 --cluster "qsub -cwd -V -o snakemake.output.log -e snakemake.error.log  -P gsi -pe smp {threads} -l h_vmem={params.memory_per_thread} -l h_rt={params.run_time} -b y "  run_SV_analysis

Support

For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .

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oicr-gsi/nanoporeRunSVAnalysis