loukesio / nextflow_LifeSciences

Nextflow for Life Sciences

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
2. Bioinformatics workflow by Andrew Severin
3. Nextflow, official site
4. Nextflow training, Seqera labs