prototype-wes-pipeline

A placeholder pipeline written in Snakemake

Installation and environment

Requirements

1. snakemake >= 5.3.1
2. pandas and numpy
3. docker (the alignment step is excuted in a samtools docker)

Running Snakemake in its own environment is described in the snakemake documentation

$ conda create --name snakemake
$ source activate snakemake
(snakemake)$ pip3 install snakemake pandas numpy
(snakemake)$ source deactivate

Running snakemake

From within your preferred Snakemake environment and within the prototype-wes-pipeline/ directory you can just run the $ snakemake command since we have a rule all written.

$ cd prototype-wes-pipeline/
$ source activate snakemake
(snakemake)$ snakemake

Structure

Rule execution

The following execution order of rules occurs:

align_sample > call_snvs > annotate_varians > merge_variants

align_samples - reads fastq pairs as and a reference as inputs. outputs per-sample bam.

call_snvs - tumor normal bam pairs and a reference as inputs. outputs a per-group vcf.

annotate_variants - per-group vcf as and a reference an inputs. outputs a per-group maf.

merge_variants - list of all per-group mafs as an input and a single merged maf as an output.

Inputs

input structure is based on current versions of the WES snakemake pipeline

Reference files locations are stored in cidc_wes/ref.yaml

Paired fastq's are listed as samples in config.yaml

Tumor-normal pairs are defined in metasheet.csv

Outputs

Outputs are stored in a results/ folder and have the following layout

results/
├── aligned
│   ├── sample-A-normal.bam
│   ├── sample-A-tumor.bam
│   ├── sample-B-normal.bam
│   └── sample-B-tumor.bam
├── annotated_variants
│   ├── groups
│   │   ├── sample-A.maf
│   │   └── sample-B.maf
│   └── merged.maf
└── variants

aligned contains the alignments of the fastq pairs stored by samples variable listed in the config.yaml

annotated_variants/groups has results listed per-run as defined as the RunName column in the metasheet.csv

annotated_variants/merged.maf has all the results for the run concatonated.

Intermediate vcf files produced and stored in results/variants/ but these are marked as temp() and thus are not maintained after the run. Removing the temp() would cause them to be retained.

Logs

Logs are stored in a logs/ folder and has the following layout

logs/
├── align
│   ├── sample-A-normal.log
│   ├── sample-A-tumor.log
│   ├── sample-B-normal.log
│   └── sample-B-tumor.log
├── annotated_variants
│   ├── groups
│   │   ├── sample-A.log
│   │   └── sample-B.log
│   └── merge.log
└── variants
    ├── sample-A.log
    └── sample-B.log