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java -version
#needs to be > version 8
curl -s https://get.nextflow.io | bash
./nextflow run hello
A simple nextflow file is this:
#!/usr/bin/env nextflow
process sayhello {
echo true
script:
"""
echo this works, hello
"""
}
There are no inputs or outputs, this just prints to the screen.
Create this (e.g. nano main.nf
, then paste in)
Run: ./nextflow run main.nf
“this works, hello” should print to screen.
#!/usr/bin/env nextflow
params.reads = "example.fa" //replace with [--reads yourfile] at run
reads_ch = Channel.fromPath(params.reads) //A channel to send the file
process thing {
echo true
input:
file x from reads_ch
script:
"""
echo yes
echo $x
"""
}
Run: ./nextflow run main.nf --reads R1.fastq