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dragenflow

https://github.com/dhslab/dragenflow

Science Score: 26.0%

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

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.4%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: dhslab
  • License: mit
  • Language: Nextflow
  • Default Branch: dev
  • Size: 111 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 2
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/dragenflow nf-core/dragenflow

Introduction

nf-core/dragenflow is a bioinformatics pipeline that runs a variety of dragen commands and workflows for downstream analysis

Pipeline Summary:

all workflows:

  • samplesheet check
  • make fasqlists (from reads/crams/bams)
  • concatenate fastqlists
  • run dragen

rna downstream analysis:

  • get sizes file and strandedness
  • annotate rnaseq
  • bedtools genomecov
  • ucsc bedclip, bedgraph to bigwig

tumor downstream analysis

  • annotate small variants

Usage

Samplesheet Format

If running with mgi samplesheet:

Pass flag --mgi true, and use Samplemap2.csv with the following columns:

csv FASTQ Path - Read 1,FASTQ Path - Read 2,Flowcell ID,Index Sequence,Flowcell Lane,ESP ID,Pool Name,Species,Illumina Sample Type,Library Type,Library Name,Date Complete,Total Reads,Total Bases,Avg >Q Score Read 1,Avg Q Score Read 2,% >Q30 Read 1,% >Q30 Read 2,PhiX Error Rate Read 1,PhiX Error Rate Read 2,% Pass Filter Clusters Read 1,% Pass Filter Clusters Read 2

If running with custom samplesheet:

First column should be id, remaining columns are data type, or a combination of data types (read1,read2/bam/cram)

Examples:

csv id,read1,read2 sample1,sample1_R1.fastq.gz,sample1_R1.fastq.gz sample2,sample2_R1.fastq.gz,sample2_R1.fastq.gz

csv id,bam,cram sample1,,sample1.cram sample2,sample2.bam,

Run Command

bash nextflow run dhslab/dragenflow -r dev \ -profile ris,<dragen2/dragen4/dragenaws> \ --input /path/to/samplesheet \ --outdir <OUTDIR> \ --workflow <rna/5mc/align/somatic/tumor/idtumis>

Optional Parameters

--dragen_args <dragen arguments> : provides additional arguments in dragen command

--mgi true : pass if mgi samplesheet is used

-bucket-dir <path to s3 bucket dir> : pass if aws is used

AWS

run the following commands:

nextflow secrets set AWSACCESSKEY <aws access key>

nextflow secrets set AWSSECRETKEY <aws secret key>

export DRAGEN_USERNAME <dragen username>

export DRAGEN_PASSWORD <dragen password>

to check if secrets are set/exist in NXF_HOME, run:

nextflow secrets list

Owner

  • Name: Code and Software from David Spencer's lab
  • Login: dhslab
  • Kind: organization
  • Email: dspencerlab@gmail.com
  • Location: United States of America

GitHub Events

Total
  • Issue comment event: 1
  • Push event: 32
  • Pull request event: 2
  • Create event: 1
Last Year
  • Issue comment event: 1
  • Push event: 32
  • Pull request event: 2
  • Create event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 days
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 days
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
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  • dhspence (3)
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Dependencies

.github/workflows/awsfulltest.yml actions
  • actions/upload-artifact v3 composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/awstest.yml actions
  • actions/upload-artifact v3 composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v3 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/clean-up.yml actions
  • actions/stale v7 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
.github/workflows/linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • mshick/add-pr-comment v1 composite
  • nf-core/setup-nextflow v1 composite
  • psf/black stable composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
.github/workflows/release-announcments.yml actions
  • actions/setup-python v4 composite
  • rzr/fediverse-action master composite
  • zentered/bluesky-post-action v0.0.2 composite
modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
pyproject.toml pypi