delly-nf

This pipeline performs INDEL calling on isotype strains versus the reference strain. The VCFs output from this pipeline are used within the lab and also released to the world via CaeNDR.

Pipeline overview

"""

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 | (  \  )| (    \/| (      | (   ( \   / )     |  \  ( || (    \/
 | |   ) || (__    | |      | |    \ (_) /_____ |   \ | || (__    
 | |   | ||  __)   | |      | |     \   /(_____)| (\ \) ||  __)   
 | |   ) || (      | |      | |      ) (        | | \   || (      
 | (__/  )| (____/\| (____/\| (____/\| |        | )  \  || )      
 (______/ (_______/(_______/(_______/\_/        |/    )_)|/       

nextflow main.nf --help

nextflow main.nf --debug

nextflow main.nf --sample_sheet=isotype_groups.tsv --species=c_elegans

nextflow main.nf --sample_sheet=isotype_groups.tsv --bam_dir=/path/to/bams --reference=/path/to/reference.fa --ref_strain=reference_strain

parameters           description                                              Set/Default
==========           ===========                                              ========================
--debug              Set to 'true' to test                                    (optional)
--sample_sheet       TSV with isotype_ref_strain column (needs header)        (required)
--minsize            The minimum size in bp to report for INDELs              (optional)
--maxsize            The maximum size in bp to report for INDELs              (optional)

--species            Species: 'c_elegans', 'c_tropicalis' or 'c_briggsae'     (required/optional)
and / or
--bam_dir            Path to folder containing bams                           (optional/required)
--ref_strain         Name of strain to use a reference (matches genome ref)   (optional/required)
--reference          Path to reference genome fasta                           (optional/required)


HELP: https://andersenlab.org/dry-guide/latest/pipelines/pipeline-delly   
----------------------------------------------------------------------------------------------

"""

Software Requirements

• The latest update requires Nextflow version 24+. On Rockfish, you can access this version by loading the nf24_env conda environment prior to running the pipeline command:

module load python/anaconda
source 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/delly-nf --debug

Running on Rockfish

You should run this in a screen or tmux session.

nextflow run -latest andersenlab/delly-nf --sample_sheet <path_to_sample_sheet> --species <species>

or

nextflow run -latest andersenlab/delly-nf --sample_sheet <path_to_sample_sheet> --bam_dir <path_to_bam_folder> --reference <path_to_reference> --ref_strain <reference_strain>

Parameters

-profile

There are three configuration profiles for this pipeline.

• rockfish - Used for running on Rockfish (default).
• quest - Used for running on Quest.

Note

If you forget to add a -profile, the rockfish profile will be chosen as default

--debug

You should use --debug for testing/debugging purposes. This will run the debug test set (located in the test_data folder).

For example:

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

Using --debug will automatically set the sample sheet to test_data/sample_sheet.tsv

--sample_sheet

A sample sheet produced by the concordance pipeline with a column specifying isotype reference strains with the column header "isotype_ref_strain".

--species (required if --bam_dir, --reference, or --ref_strain not specified, otherwise optional)

Options: c_elegans, c_briggsae, or c_tropicalis

--bam_dir (required if --species not specified, otherwise optional)

Path to the folder containing species strain bams.

--reference (required if --species not specified, otherwise optional)

Path to the reference strain fasta file.

--ref_strain (required if --species not specified, otherwise optional)

The name of the reference strain to call indels against

--minsize (optional)

The minimum size cutoff for reporting an insertion or deletion (default: 50bp)

--maxsize (optional)

The maximum size cutoff for reporting an insertion or deletion (default: 1000bp)

-output-dir (optional)

default - results

A directory in which to output results

Output

└── results
    ├── workflow_software_versions.txt
    └── indels
        ├── AB1_indels.vcf.gz
        ├── AB1_indels.vcf.gz.tbi
        ├── AB4_indels.vcf.gz
        ├── AB4_indels.vcf.gz.tbi
        ├── MY23_indels.vcf.gz
        ├── MY23_indels.vcf.gz.tbi
        ...

Relevant Docker Images

• dellytools/delly (link)
• quay.io/biocontainers/bcftools (link)

Note: If running on Rockfish, make sure to properly set up Nextflow prior to running workflow (Nextflow configuration).