https://github.com/loukesio/nextflow_lifesciences

https://github.com/loukesio/nextflow_lifesciences

Last synced: 4 days ago
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• Host: GitHub
• URL: https://github.com/loukesio/nextflow_lifesciences
• Owner: loukesio
• License: gpl-3.0
• Created: 2023-08-02T13:39:26.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2023-09-19T14:39:46.000Z (over 1 year ago)
• Last Synced: 2023-09-19T17:15:12.005Z (over 1 year ago)
• Size: 29.3 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
Nextflow  for Life Sciences


[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.27.6-brightgreen.svg)](https://www.nextflow.io/)

![Twitter Follow](https://img.shields.io/twitter/follow/loukesio)

![Javascript](https://img.shields.io/badge/logo-javascript-blue?logo=javascript)

Nextflow for RNA-seq


### 1. Check the quality of the fastq.gz files  

```

#!/usr/bin/env nextflow

nextflow.enable.dsl=2

// Input/output paths

params.input = '/netscratch/dep_tsiantis/grp_tsiantis/1_CURRENT_LAB_MEMBERS/LTheodosiou/Projects/GROseq/RNAseq/raw_data'

params.output = '/netscratch/dep_tsiantis/grp_tsiantis/1_CURRENT_LAB_MEMBERS/LTheodosiou/Projects/GROseq/RNAseq/test_nextflow'

process fastqc {

    input:

    path reads

    output:

    path("${params.output}/fastqc_raw/*") into ch_fastqc

    script:

    """

    . "/netscratch/dep_tsiantis/grp_tsiantis/1_CURRENT_LAB_MEMBERS/LTheodosiou/Software/Anaconda3/etc/profile.d/conda.sh"

    conda activate fastqc

    mkdir -p ${params.output}/fastqc_raw

    fastqc $reads -o ${params.output}/fastqc_raw/

    """

}

workflow {

    readsChannel = Channel.fromPath("${params.input}/*.fastq")

    fastqc(readsChannel)

}

```

### References 

Here are some key links that can help you build your own Nextflow pipelines 


**1.** [Carpentries material from Physalia courses](https://carpentries-incubator.github.io/workflows-nextflow/index.html) 


**2.** [Bioinformatics workflow by Andrew Severin](https://bioinformaticsworkbook.org/dataAnalysis/nextflow/02_creatingAworkflow.html) 


**3.** [Nextflow, official site](https://training.nextflow.io/hands_on/04_implementation/#process-4-gatk-recalibrate) 


**4.** [Nextflow training, Seqera labs](https://training.seqera.io/#_gitpod)