mutation-signature-nf

A pipeline to do mutation signature analysis using signature.tools.lib. This can take a list of VCF files as input and process them individually.

Steps -

1. Detect the VCF files coming from a perticlar tool (currently supported ones listed below)
2. Pre-processing and filtration of VCF files based on from which tools they coming from. This also standardise the vcf files going into downstream prcoessing.
3. Runs the signature-fit function based on organ-specific signatures.

Usgae

A basic command to run this pipeline

nextflow run main.nf --input testdata/input_mix_vcf_origin.tsv --organ "Colorectal" -with-docker

Take a look at testdata/input_mix_vcf_origin.tsv

stdout after running the above command -

N E X T F L O W  ~  version 20.01.0
Launching `main.nf` [exotic_northcutt] - revision: fb872d5257
Launch dir        : /home/ec2-user/mutational-signature-nf
Working dir       : /home/ec2-user/mutational-signature-nf/work
Script dir        : /home/ec2-user/mutational-signature-nf
User              : ec2-user
Input             : testdata/input_mix_vcf_origin.tsv
Output dir        : results
organ             : Colorectal
bootstrap         : true
----------------------------------------------------
executor >  local (7)
[2f/5069b7] process > obtain_pipeline_metadata [100%] 1 of 1 ✔
[82/25f847] process > detect_vcf_origin_tool   [100%] 2 of 2 ✔
[6e/d3018c] process > prepare_vcf              [100%] 2 of 2 ✔
[6f/c71c15] process > signature_fit            [100%] 2 of 2 ✔
Completed at: 05-Apr-2022 12:45:49
Duration    : 1m 6s
CPU hours   : (a few seconds)
Succeeded   : 7

Parameters

param	default	description
input	null	A TSV file with samples to be analysed. More details here
organ	"Breast"	Which organ-specific signatures will be used in analysis. Complete list can be found here
bootstrap	true	Request signature fit with bootstrap
genome_version	hg38	Genome version to use, Options - hg19 or hg38
signaturefit_options	null	Additional signaturefit options as a string
preparedata_options	null	Additional preparedata options as a string

Input

A TSV file with two columns with headers

sample_name	vcf_file_path

sample_name    vcf_file_path
sample_1    path_to_vcf1
sample_2    path_to_vcf2

Currently supported VCF file from tools

• manta
• strelka

Supported organs

For -O, --organ=ORGAN option possible values -

If SIGVERSION is COSMICv2 or COSMICv3.2, then a selection of signatures found in the given organ will be used. Available organs depend on the selected SIGVERSION. For RefSigv1 or RefSigv2 -

1. Biliary
2. Bladder
3. Bone_SoftTissue
4. Breast
5. Cervix (v1 only)
6. CNS
7. Colorectal
8. Esophagus
9. Head_neck
10. Kidney
11. Liver
12. Lung
13. Lymphoid
14. NET (v2 only)
15. Oral_Oropharyngeal (v2 only)
16. Ovary
17. Pancreas
18. Prostate
19. Skin
20. Stomach
21. Uterus

Ref - From helpmenu

License Agreements

This pipeline utilizes third-party tools or databases that may have their own license agreements. It is important to acknowledge and comply with the terms and conditions set forth by these dependencies. Please refer to their respective documentation and licenses for more information.

• signature.tools.lib R package