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
java -jar cromwell.jar run nanoporeRunSVAnalysis.wdl --inputs inputs.json
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 |
Parameter | Value | Default | Description |
---|
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 |
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 |
This section lists command(s) run by nanoporerunsvanalysis workflow
- Running nanoporerunsvanalysis
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
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
For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .
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