nanoporeCoverageAnalysis

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

Overview

Dependencies

• nanopore_sv_analysis 20220505
• hg38-nanopore-sv-reference

Usage

Cromwell

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

Inputs

Required workflow parameters:

Parameter	Value	Description
sample	String	name of sample
normal	String	name of the normal sample
tumor	String	name of the tumor sample
samplefile	File	sample file
coverageAnalysis.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
coverageAnalysis.jobMemory	Int	32	memory allocated for Job
coverageAnalysis.timeout	Int	24	Timeout in hours, needed to override imposed limits

Outputs

Output	Type	Description	Labels
depth100window	File	output from rule run_coverage_analysis of the original workflow	vidarr_label: depth100window
depth1000window	File	output from rule run_coverage_analysis of the original workflow	vidarr_label: depth1000window
depth10000window	File	output from rule run_coverage_analysis of the original workflow	vidarr_label: depth10000window
depth100000window	File	output from rule run_coverage_analysis of the original workflow	vidarr_label: depth100000window
depth500000window	File	output from rule run_coverage_analysis of the original workflow	vidarr_label: depth500000window
plotDepth	File	output from rule run_coverage_analysis of the original workflow	vidarr_label: plotDepth
plotSmall	File	output from rule run_coverage_analysis of the original workflow	vidarr_label: plotSmall
plotLarge	File	output from rule run_coverage_analysis of the original workflow	vidarr_label: plotLarge
plotDepthChrms	Array[File]	output from rule run_coverage_analysis of the original workflow	vidarr_label: plotDepthChrms

Commands

This section lists command(s) run by nanoporeCoverageAnalysis workflow

• Running nanoporeCoverageAnalysis

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 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_coverage_analysis
 

Support

For support, please file an issue on the Github project or send an email to [email protected] .

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