gtcheck-nf

This pipeline performs a comparison of new sample variants against existing samples to verify identity.

Pipeline overview

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 `.__. |   `.__.    `.__,'   (___)(___)  `.__.'   `.__,'   (___ ) (___)             (___)(___) (___)     
 ( `-' ;                                                                                                 
  `.__.                                                                                               

nextflow main.nf --species=c_elegans --release=20250331 --sample_sheet=/path/to/sample/sheet --sample_dir=/path/to/samples -output-dir=/path/to/results

nextflow main.nf --strain_dir=/path/to/strain/vcfs --sample_sheet=/path/to/sample/sheet --sample_dir=/path/to/samples -output-dir=/path/to/results

    parameters           description                                              Set/Default
    ==========           ===========                                              ========================
    --help                Set to 'true' for usage                                 false
    --species             Species: 'c_elegans', 'c_tropicalis' or 'c_briggsae'    (required if strain_dir not defined)
    --release             CaeNDR release for genome lookup values                 (required if strain_dir not defined)
    --sample_sheet        Sheet listing strain and sample vcf names, one per line (required)
    --sample_dir          Path to sample directory                                (required)
    --strain_dir          Path to strain vcf directory                            (required if species or release no defined)
    -output-dir           Output destination directory                            GTcheck_{date}

    username                                                                      ${"whoami".execute().in.text}

Software Requirements

• The latest update requires Nextflow version 24.10.0+. On Rockfish, you can access this version by loading the nf24_env conda environment prior to running the pipeline command:

ml anaconda
conda activate /data/eande106/software/conda_envs/nf24_env

Usage

Note: if you are having issues running Nextflow or need reminders, check out the Nextflow page.

Testing on Rockfish

This command uses a test dataset

nextflow run -latest andersenlab/gtcheck-nf --debug

Note

This is not currently implemented

Running on Rockfish

You should run this in a screen or tmux session.

nextflow andersenlab/gtcheck-nf --species=c_elegans --release=20250331 --sample_sheet=/path/to/sample/sheet --sample_dir=/path/to/sample/dir

General Parameters

--species (optional if strain_dir specified)

If the directory containing strain VCFs is not specified, the species and release date can be used to look up existing files for c_elegans, c_briggsae, or c_tropicalis

--release (optional if strain_dir specified)

If the directory containing strain VCFs is not specified, the species and release date can be used to look up existing files for c_elegans, c_briggsae, or c_tropicalis

--sample_sheet (optional)

Path to sample sheet containing list of sample names for comparison

--sample_dir (required)

Path to folder containing sample VCF files

--vcf (optional if species and release are specified)

Path to strain VCF file

--strain_sheet (optional)

Path to strain sheet containing list of sample names for comparison

-output-dir (default: GTcheck_{date})

Output destination directory

Output

├── gtcheck.txt
├── gtcheck.pdf
└── versions.txt

Relevant docker images

• quay.io-biocontainers-bcftools-1.16--hfe4b78e_1 (link): Docker image maintained by Biocontainer for BCFtools
• andersenlab/numpy (link): Docker image is created within this pipeline using GitHub actions. Whenever a change is made to env/Dockerfile or .github/workflows/build_docker.yml GitHub actions will create a new docker image and push if successful

Make sure that you have followed the Nextflow configuration described in the dry-guide prior to running the workflow.