/nanoporeSVAll

Workflow for executing all task of nanopore filterfastq, nanopore mapping, nanopore coverage analysis, nanopore structural variants analysis, wdl wrapper for snakemake workflow forked from Simpson Lab repo.

Primary LanguageWDL

nanoporeSVAll

nanoporeSVAll, workflow that generates structural variant and coverage analysis 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 nanoporeSVAll.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 String sample file
smkConfig.generateConfig_modules String modules needed to run generateConfig
SVAll.modules String Names and versions of modules

Optional workflow parameters:

Parameter Value Default Description

Optional task parameters:

Parameter Value Default Description
smkConfig.generateConfig_timeout Int 24 Timeout in hours, needed to override imposed limits
smkConfig.generateConfig_jobMemory Int 8 memory allocated for Job
SVAll.jobMemory Int 32 memory allocated for Job
SVAll.timeout Int 24 Timeout in hours, needed to override imposed limits

Outputs

Output Type Description Labels
insertions File output from rule all of the original workflow vidarr_label: insertions
deletions File output from rule all of the original workflow vidarr_label: deletions
duplications File output from rule all of the original workflow vidarr_label: duplications
inversions File output from rule all of the original workflow vidarr_label: inversions
translocations File output from rule all of the original workflow vidarr_label: translocations
CNVs File output from rule all of the original workflow vidarr_label: CNVs
depth100window File output from rule all of the original workflow vidarr_label: depth100window
depth1000window File output from rule all of the original workflow vidarr_label: depth1000window
depth10000window File output from rule all of the original workflow vidarr_label: depth10000window
depth100000window File output from rule all of the original workflow vidarr_label: depth100000window
depth500000window File output from rule all of the original workflow vidarr_label: depth500000window
plotDepth File output from rule all of the original workflow vidarr_label: plotDepth
plotSmall File output from rule all of the original workflow vidarr_label: plotSmall
plotLarge File output from rule all of the original workflow vidarr_label: plotLarge
plotDepthChrms Array[File] output from rule all of the original workflow vidarr_label: plotDepthChrms

Commands

This section lists command(s) run by nanoporesvall workflow

  • Running nanoporesvall
         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 "

Support

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

Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)