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dnaaln

ICGC ARGO Workflow for DNA-Seq Alignment

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

Science Score: 31.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

ICGC ARGO Workflow for DNA-Seq Alignment

Basic Info
  • Host: GitHub
  • Owner: icgc-argo-workflows
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Size: 60.5 MB
Statistics
  • Stars: 0
  • Watchers: 11
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 3 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog License Citation

docs/README.md

nfcore/dnaseqaln: Documentation

The nfcore/dnaseqaln documentation is split into the following pages:

  • Usage Alignment starting from local sequencing payload via BWA nextflow run main.nf -profile debug_qa,docker --api_token NNNNNNNN-NNNN-NNNN-NNNN-NNNNNNNNNNNN --local_sequencing_json test/data/local_sequencing.json --local_data_directory test/data --local true --reference_fasta test/reference/GRCh38_Verily_v1.fasta --tools bwamem_aln,markdup,cleanup Alignment starting from local sequencing payload via BWA2 nextflow run main.nf -profile debug_qa,docker --api_token NNNNNNNN-NNNN-NNNN-NNNN-NNNNNNNNNNNN --local_sequencing_json test/data/local_sequencing.json --local_data_directory test/data --local true --reference_fasta test/reference/GRCh38_Verily_v1.fasta --tools bwamem2_aln,markdup,cleanup Alignment and upload starting from local sequencing payload via both BWA and BWA2 nextflow run main.nf -profile debug_qa,docker --api_token NNNNNNNN-NNNN-NNNN-NNNN-NNNNNNNNNNNN --local_sequencing_json test/data/local_sequencing.json --local_data_directory test/data --local true --reference_fasta test/reference/GRCh38_Verily_v1.fasta --tools bwamem2_aln,bwamem2_aln,markdup,up_qc,up_aln,cleanup Alignment and upload starting from local sequencing payload via both BWA and BWA2 without markdup nextflow run main.nf -profile debug_qa,docker --api_token NNNNNNNN-NNNN-NNNN-NNNN-NNNNNNNNNNNN --local_sequencing_json test/data/local_sequencing.json --local_data_directory test/data --local true --reference_fasta test/reference/GRCh38_Verily_v1.fasta --tools bwamem2_aln,bwamem2_aln,up_aln,cleanup Alignment starting from SONG/SCORE nextflow run main.nf -profile debug_qa,docker --api_token NNNNNNNN-NNNN-NNNN-NNNN-NNNNNNNNNNNN --analysis_id 026e7dbd-8a7b-4ee1-ae7d-bd8a7b0ee120 --study_id TEST-QA --tools bwamem2_aln,bwamem2_aln,up_aln,cleanup --reference_fasta test/reference/GRCh38_Verily_v1.fasta Alignment starting from SONG/SCORE w/ Indexing nextflow run main.nf -profile debug_qa,docker --api_token NNNNNNNN-NNNN-NNNN-NNNN-NNNNNNNNNNNN --analysis_id 026e7dbd-8a7b-4ee1-ae7d-bd8a7b0ee120 --study_id TEST-QA --tools index,bwamem2_aln,bwamem2_aln,up_aln,cleanup --reference_fasta test/reference/GRCh38_Verily_v1.fasta
  • Output
    • An overview of the different results produced by the pipeline and how to interpret them.

Owner

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

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

Citation (CITATIONS.md) 

# nfcore/dnaseqaln: 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/)

- [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)

- [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.

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