Version 3+

Technical Document

Scope of Work

Central to processing is the UCGD concept of scope_of_work which is defined into the following subtypes and used as Nextflow -entry options

Nextflow entry options
VAR
DGN
RNA
SV
JGT
MOSAIC
POST_PROCESS

VAR & DGN will run all steps of the pipeline, including SV, JGT, MOSAIC and POST_PROCESS steps, however SV, JGT, MOSAIC and POST_PROCESS can be run independently if required input files are present.

Directory outlines

The final data locations will remain the same (including read-only permission).

Final project directories:

./scratch/ucgd/lustre/UCGD_Datahub/IRBs/[IRB]/[PROJECT]/UCGD
└── GRCh38
    ├── Analysis
    ├── Data
    │   └── PolishedCrams
    ├── Reports
    │   ├── alignstats
    │   ├── fastp
    │   ├── goleft
    │   ├── manta
    │   ├── mosaic
    │   ├── peddy
    │   ├── runlogs
    │   └── stats
    ├── RNASeq
    │   ├── Data
    │   │   ├── Kallisto
    │   │   └── StarBams
    │   └── Reports
    │       ├── alignstats
    │       ├── fastp
    │       ├── kallisto
    │       ├── leafcutter
    │       ├── outrider
    │       ├── rnaqc
    │       └── star
    └── VCF
        ├── Complete
        ├── GVCFs
        ├── Manta
        └── Smoove

Project scratch directory

./scratch/ucgd/lustre/UCGD_Datahub/IRBs/[IRB]/[PROJECT]/Scratch
├── modules
│   └── local
│       ├── alignstats
│       │   └── main.nf
│       ├── bcftools
│       │   ├── concat
│       │   │   └── main.nf
│       │   ├── merge
│       │   │   └── main.nf
│       │   ├── norm
│       │   │   └── main.nf
│       │   ├── stats
│       │   │   └── main.nf
│       │   └── view
│       │       └── main.nf
│       ├── fastp
│       │   └── main.nf
│       ├── fastqforward
│       │   ├── bam2gvcf
│       │   │   └── main.nf
│       │   └── fastq2bam
│       │       └── main.nf
│       ├── goleft
│       │   └── indexcov
│       │       └── main.nf
│       ├── kallisto
│       │   └── main.nf
│       ├── leafcutter
│       │   ├── bam_to_junc.nf
│       │   ├── intron_clustering.nf
│       │   └── leafcutter_md.nf
│       ├── manta
│       │   └── main.nf
│       ├── mosaic
│       │   ├── api
│       │   │   └── main.nf
│       │   ├── cli
│       │   │   └── main.nf
│       │   └── template
│       │       └── main.nf
│       ├── multiqc
│       │   └── main.nf
│       ├── outrider
│       │   └── outrider.nf
│       ├── peddy
│       │   └── main.nf
│       ├── qc
│       │   ├── rnaseqc.nf
│       │   └── run_fastqc.nf
│       ├── samtools
│       │   └── view
│       │       └── main.nf
│       ├── sentieon
│       │   ├── gvcftyper
│       │   │   └── main.nf
│       │   └── varcal
│       │       └── main.nf
│       ├── slivar
│       │   └── main.nf
│       ├── smoove
│       │   └── main.nf
│       ├── spot
│       │   └── spot.nf
│       ├── star
│       │   ├── generate_star_index.nf
│       │   ├── merge_counts.nf
│       │   └── run_star.nf
│       ├── ucgdtools
│       │   └── main.nf
│       └── vep
│           └── main.nf
├── subworkflows
│   └── local
│       ├── alignment.nf
│       ├── annotations.nf
│       ├── gvcf_generate.nf
│       ├── input_preprocess.nf
│       ├── qc_cram.nf
│       ├── qc_fastq.nf
│       ├── qc_rna.nf
│       ├── qc_vcf.nf
│       ├── sentieon_vc.nf
│       └── slivar.nf
├── ucgd_main.nf
├── ucgd.master.config
├── ucgd_post_params.yaml
└── workflows
    └── local
        ├── jgt.nf
        ├── mosaic.nf
        ├── neo.nf
        ├── project.nf
        ├── rna.nf
        ├── sv.nf
        └── var.nf

Component description

Nextflow file	Description
ucgd_main.nf	The main entry point script contains all -entry options.
ucgd.master.config	Contains all templated paths and definitions.
ucgd_post_params.yaml	Parameter file used to define and initiate launching of post processing steps.
ucgd_versions.yml	Created by the pipeline post processing. Will contain all software versions for posterity.

Processing Overview

Pipeline DAG visualisation

Version Notes

Version 3.24.115 Update:

Pipeline has been updated to process using DeepVariant and GLnexus. Sentieon and NeoSeq processing has been removed and archived. All NeoSeq modules remain archived. Neoseq nextflow profile had been moved to priority for future use.

Major changes from Version 2:

• Migration to Nextflow's DSL2 framework, which allows an improved ability to modularize and compartmentalize Nextflow processes and code.
• Nextflow process to occur and remain within the [IRB]/[PROJECT]/Scratch location.
• Reference GRCh38 is the default and only reference used.
• Processing based on UCGD scope_of_work.