nanoporeMapping

nanoporMapping, workflow that generates b_allele_frequency.bed file 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 nanoporeMapping.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
`mapping.modules`	String	Names and versions of modules

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
`mapping.jobMemory`	Int	8	memory allocated for Job
`mapping.timeout`	Int	24	Timeout in hours, needed to override imposed limits

Outputs

Output	Type	Description	Labels
`bAlleleFrequency`	File	output from rule mapping of the original workflow	vidarr_label: bAlleleFrequency

Commands

This section lists command(s) run by nanoporemapping workflow

Running nanoporemapping

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 the 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 8 --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 "  mapping

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/nanoporeMapping