xml_variant_ingestion

ICGC ARGO variant calling pipeline which digest xml to vcf variant format

https://github.com/icgc-argo-workflows/xml_variant_ingestion

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (3.5%) to scientific vocabulary

Last synced: 10 months ago · JSON representation ·

Repository

ICGC ARGO variant calling pipeline which digest xml to vcf variant format

Basic Info

Host: GitHub
Owner: icgc-argo-workflows
License: agpl-3.0
Language: Python
Default Branch: main
Size: 2.48 MB

Statistics

Stars: 0
Watchers: 10
Forks: 0
Open Issues: 2
Releases: 0

Created almost 2 years ago · Last pushed 12 months ago

Metadata Files

Readme Changelog License Code of conduct Citation

Input data:

Mapping file: test/data/sample_new.tsv

XML file: test/data/example.xml

Reference files:

test/reference/

hg19.fa Not provided, download needed https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz

hg19.fa.fai

hg38.fa.gz Not provided, download needed https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz

hg38.fa.fai

hg38.dict

hg19ToHg38.over.chain.gz https://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz

Usage

Download hg19.fa and hg38.fa.gz to test/reference/
Retrive api_token
Workflow command

Minimal Test bash nextflow run main.nf \ -profile docker,test,rdpc_qa \ --api_token NNNNNNN \ --hg19_ref_fa /PATH/TO/hg19.fa \ --hg19_ref_fai /PATH/TO/hg19.fa.fai \ --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \ --hg38_ref_fa /PATH/TO/hg38.fa.gz \ --hg38_ref_fai /PATH/TO/hg38.fa.fai \ --hg38_ref_dict /PATH/TO/hg38.dict Test in RDPC-QA bash nextflow run main.nf \ -profile docker,rdpc_qa,test_rdpc_qa \ --api_token NNNNNNN \ --xml /PATH/TO/XML.FILE \ --experiment_info_tsv /PATH/TO/MAPPING.TSV \ --hg19_ref_fa /PATH/TO/hg19.fa \ --hg19_ref_fai /PATH/TO/hg19.fa.fai \ --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \ --hg38_ref_fa /PATH/TO/hg38.fa.gz \ --hg38_ref_fai /PATH/TO/hg38.fa.fai \ --hg38_ref_dict /PATH/TO/hg38.dict

Test data (Original)

bash nextflow run main.nf \ -profile docker,rdpc_qa,test_rdpc_qa \ --api_token NNNNNNN \ --xml ./test/data/example.xml \ --experiment_info_tsv ./test/data/sample_new.tsv \ --hg19_ref_fa /PATH/TO/hg19.fa \ --hg19_ref_fai /PATH/TO/hg19.fa.fai \ --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \ --hg38_ref_fa /PATH/TO/hg38.fa.gz \ --hg38_ref_fai /PATH/TO/hg38.fa.fai \ --hg38_ref_dict /PATH/TO/hg38.dict

Test data ( Test1 - ORD-0000001-01.xml - short-variants/copy-number-alterations )

bash nextflow run main.nf \ -profile docker,rdpc_qa,test_rdpc_qa \ --api_token NNNNNNN \ --xml ./test/data/ORD-0000001-01.xml \ --experiment_info_tsv ./test/data/sample_1.tsv \ --hg19_ref_fa /PATH/TO/hg19.fa \ --hg19_ref_fai /PATH/TO/hg19.fa.fai \ --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \ --hg38_ref_fa /PATH/TO/hg38.fa.gz \ --hg38_ref_fai /PATH/TO/hg38.fa.fai \ --hg38_ref_dict /PATH/TO/hg38.dict

Test data ( Test2 - ORD-0000002-01.xml - short-variants )

bash nextflow run main.nf \ -profile docker,rdpc_qa,test_rdpc_qa \ --api_token NNNNNNN \ --xml ./test/data/ORD-0000002-01.xml \ --experiment_info_tsv ./test/data/sample_2.tsv \ --hg19_ref_fa /PATH/TO/hg19.fa \ --hg19_ref_fai /PATH/TO/hg19.fa.fai \ --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \ --hg38_ref_fa /PATH/TO/hg38.fa.gz \ --hg38_ref_fai /PATH/TO/hg38.fa.fai \ --hg38_ref_dict /PATH/TO/hg38.dict

Test data ( Test3 - ORD-0000003-01.xml - short-variants )

bash nextflow run main.nf \ -profile docker,rdpc_qa,test_rdpc_qa \ --api_token NNNNNNN \ --xml ./test/data/ORD-0000003-01.xml \ --experiment_info_tsv ./test/data/sample_3.tsv \ --hg19_ref_fa /PATH/TO/hg19.fa \ --hg19_ref_fai /PATH/TO/hg19.fa.fai \ --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \ --hg38_ref_fa /PATH/TO/hg38.fa.gz \ --hg38_ref_fai /PATH/TO/hg38.fa.fai \ --hg38_ref_dict /PATH/TO/hg38.dict

Test data ( Test4 - ORD-0000004-01.xml - short-variants )

bash nextflow run main.nf \ -profile docker,rdpc_qa,test_rdpc_qa \ --api_token NNNNNNN \ --xml ./test/data/ORD-0000004-01.xml \ --experiment_info_tsv ./test/data/sample_4.tsv \ --hg19_ref_fa /PATH/TO/hg19.fa \ --hg19_ref_fai /PATH/TO/hg19.fa.fai \ --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \ --hg38_ref_fa /PATH/TO/hg38.fa.gz \ --hg38_ref_fai /PATH/TO/hg38.fa.fai \ --hg38_ref_dict /PATH/TO/hg38.dict

Test data ( Test5 - ORD-0000005-01.xml - short-variants/copy-number-alterations/rearrangements )

bash nextflow run main.nf \ -profile docker,rdpc_qa,test_rdpc_qa \ --api_token NNNNNNN \ --xml ./test/data/ORD-0000005-01.xml \ --experiment_info_tsv ./test/data/sample_5.tsv \ --hg19_ref_fa /PATH/TO/hg19.fa \ --hg19_ref_fai /PATH/TO/hg19.fa.fai \ --hg19_to_hg38_chain /PATH/TO/hg19ToHg38.over.chain.gz \ --hg38_ref_fa /PATH/TO/hg38.fa.gz \ --hg38_ref_fai /PATH/TO/hg38.fa.fai \ --hg38_ref_dict /PATH/TO/hg38.dict

Owner

Name: ICGC ARGO Workflows
Login: icgc-argo-workflows
Kind: organization
Location: Toronto, Ontario

Website: https://www.icgc-argo.org
Repositories: 26
Profile: https://github.com/icgc-argo-workflows

Home of the ICGC ARGO (Accelerate Research in Genomic Oncology) Data Platform Scientific Workflows

Citation (CITATIONS.md)

# nf-core/variantcall: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

GitHub Events

Total

Issues event: 2
Issue comment event: 2
Push event: 10
Pull request event: 4
Pull request review event: 10
Pull request review comment event: 8
Create event: 2

Last Year

Issues event: 2
Issue comment event: 2
Push event: 10
Pull request event: 4
Pull request review event: 10
Pull request review comment event: 8
Create event: 2

Dependencies

modules/icgc-argo-workflows/score/upload/meta.yml cpan

modules/icgc-argo-workflows/song/manifest/meta.yml cpan

modules/icgc-argo-workflows/song/publish/meta.yml cpan

modules/icgc-argo-workflows/song/submit/meta.yml cpan

modules/nf-core/picard/liftovervcf/meta.yml cpan

subworkflows/icgc-argo-workflows/song_score_upload/meta.yml cpan

pyproject.toml pypi

modules/nf-core/picard/liftovervcf/environment.yml pypi

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science