wf-vsnp's Introduction

vSNP3 Workflow

This Nextflow workflow is an implementation of vSNP3. See their GitHub repository for other uses that may not be implemented here.

A schematic of the steps in the workflow.

Requirements

Nextflow
Docker or Singularity

Install

git clone https://github.com/gregorysprenger/wf-vsnp.git

Run Workflow

Example data and dependencies are included in assets/test_data directory.

nextflow run \
-profile singularity main.nf \
--inpath assets/test_data \
--refpath assests/test_data/refs \
--vcfpath assets/test_data/vcf \
--outpath results

Test data is from USDA-VS / vsnp3_test_dataset.

# Obtain test data
git clone https://github.com/USDA-VS/vsnp3_test_dataset.git

# Move reference datafiles to assets/test_data/refs
mv vsnp3_test_dataset/vsnp_dependencies/Mycobacterium_AF2122/* wf-vsnp/assets/test_data/refs

# Move test files to assets/test_data
mv vsnp3_test_dataset/vsnp_dependencies/AF2122_test_files/step1/* wf-vsnp/assets/test_data

# Move VCF files to assets/test_data/vcf
mv vsnp3_test_dataset/vsnp_dependencies/AF2122_test_files/step2/* wf-vsnp/assets/test_data/vcf

For Aspen Cluster - Set up Singularity PATH

# Add to $HOME/.bashrc
SINGULARITY_BASE=/scicomp/scratch/$USER
export SINGULARITY_TMPDIR=$SINGULARITY_BASE/singularity.tmp
export SINGULARITY_CACHEDIR=$SINGULARITY_BASE/singularity.cache
export NXF_SINGULARITY_CACHEDIR=$SINGULARITY_BASE/singularity.cache
mkdir -pv $SINGULARITY_TMPDIR $SINGULARITY_CACHEDIR

Reload .bashrc

source ~/.bashrc

Load nextflow

module load nextflow

wf-vsnp's People

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wf-vsnp's Issues

Identifying SNP groups

Current behavior

vSNP3 is not identifying the files in assets/test_data/refs and results in the following:

Defining SNPs: None
Metadata: None
Remove From Analysis: None
gbks: No gbk

Expected behavior

The following are identified (simplified format below):

Defining SNPs: assets/test_data/refs/*filter.xlsx
Metadata: assets/test_data/refs/*metadata.xlsx
Remove From Analysis: None
gbks: assets/test_data/refs/*.gbk

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