#!/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)
}
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