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meltzerlab_nextflow_pipeline

MeltzerLab data processing Nextflow pipeline

https://github.com/ccrgeneticsbranch/meltzerlab_nextflow_pipeline

Science Score: 44.0%

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
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    .zenodo.json file
    Found .zenodo.json file
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    Scientific vocabulary similarity
    Low similarity (11.6%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

MeltzerLab data processing Nextflow pipeline

Basic Info
  • Host: GitHub
  • Owner: CCRGeneticsBranch
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Size: 647 KB
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 0
  • Open Issues: 5
  • Releases: 2
Created over 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

Meltzerlab Data Processing Pipeline

This repository contains a Nextflow based DNA/RNA data processing pipeline built specifically for Meltzer lab. This pipeline is built to run variant filtering and extensive QC on a sequencing run. The pipeline supports processing data from multiple references. We currently support

| Genome | Version | |--------|------------------| | Human | hg19, hg38 | | Mouse | mm10, mm39 | | Dog | canFam3, canFam6 |

Pipeline Overview

Meltzarlab_dataProcessing_workflow (1)

This pipeline is developed and deployed solely on NIH Biowulf.

Biowulf

This pipeline is hosted under /data/GBNCI directory. You'll need to start an interactive session inorder to launch the pipeline.

sinteractive --mem=30g --cpus-per-task=4

Usage

``` Usage: /data/GBNCI/MeltzerLabNextflowpipeline/nf.sh

This script requires one positional argument: : Provide the full path to the samplesheet in a Meltzer lab accepted format. eg: /data/GBNCI/MeltzerLabNextflowpipeline/nf.sh /data/GBNCI/DATA/VG_test/samplesheet.tsv

```

Input Samplesheet

Input file is a tab seperated samplesheet file from Meltzer lab. However the pipeline can be launched as long as these columns are present. Here is an example of the expected format.

| flowcell | library | sampletype | genome | read1 | read2 | capturetargets | |----------|---------------|-------------|--------|-------------------------|--------------------------|-----------------------------| | AAZ123 | L080123RNA | Total RNA | hg19 | L080123RNAR1.fastq.gz | L080123RNAR1.fastq.gz | APCTP53BACKlenowBait |

Help & Contributing

Come across a bug? Open an issue and include a minimal reproducible example.

Have a question? Ask it in discussions.

Want to contribute to this project? Check out the contributing guidelines.

References

This repo was originally generated from the CCBR Nextflow Template. The template takes inspiration from nektool[^1] and the nf-core template. If you plan to contribute your pipeline to nf-core, don't use this template -- instead follow nf-core's instructions[^2].

[^1]: nektool https://github.com/beardymcjohnface/nektool [^2]: instructions for nf-core pipelines https://nf-co.re/docs/contributing/tutorials/creatingwithnf_core

Owner

  • Name: CCR Genetics Branch
  • Login: CCRGeneticsBranch
  • Kind: organization

Genomics, and epigenetic pipelines developed by the OncoGenomics Section of the Genetics Branch, CCR.

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "Please cite TOOL_NAME as below." # TODO set up Zenodo to archive your tool and assign a DOI. Or if TOOL_NAME gets published in a journal, include the citation here.
authors: # TODO: author names should match those in pyproject.toml
  - family-names: LASTNAME1
    given-names: FIRSTNAME1
  - family-names: Sovacool
    given-names: Kelly
  - family-names: Koparde
    given-names: Vishal
title: "TOOL_NAME: insert one-line description here" # TODO: citation title should match pyproject.toml
version: 0.1.0 # TODO: this should be the same as in the VERSION file
date-released: 2023-08-28 # TODO update release date

GitHub Events

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Dependencies

.github/workflows/build_mkdocs.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
docs/requirements.txt pypi
  • mkdocs-git-revision-date-localized-plugin ==1.2.0
  • mkdocs-git-revision-date-plugin ==0.3.2
  • mkdocs-material ==9.1.6
  • mkdocs-material-extensions ==1.1.1
  • mkdocs-minify-plugin ==0.6.4
pyproject.toml pypi
  • Click >= 8.1.3
  • nextflow >= 0.4.0
  • pyyaml >= 6.0
setup.py pypi