'How to declare a new Nextflow variable in a shell block?
I am currently writing my first Nextflow pipeline and I try to declare a new Nextflow variable in a script but I don't manage doing it.
I would like to set up a variable, min_length, with a value read in a text file (parsed with awk) and use this value later in my pipeline as a parameter. This is what I've tried :
process get_min_len{
input:
file "./foo.tab"
output:
val length_min into min_len_channel
shell:
"""
!{length_min}=`awk '{if (\$1=="!{params.bar}") {print \$2}}' ./foo.tab`
"""
}
I get this error message :
Error executing process > 'get_min_max_len'
Caused by:
No such variable: length_min
(I also tried to initialize min_length like so : min_length=0 but it does not work either.)
Is there a way to do that ? Thanks !
Sources
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