nextflow: change part of the script basing on a parameter - nextflow

Question

I have a Nextflow workflow that's like this (reduced):
params.filter_pass = true
// ... more stuff
process concatenate_vcf {
cpus 6
input:
file(vcf_files) from source_vcf.collect()
file(tabix_files) from source_vcf_tbi.collect()
output:
file("assembled.vcf.gz") into decompose_ch
script:
"""
echo ${vcf_files} | tr " " "\n" > vcflist
bcftools merge \
-l vcflist \
-m none \
-f PASS,. \
--threads ${task.cpus} \
-O z \
-o assembled.vcf.gz
rm -f vcflist
"""
}
Now, I want to add the -f PASS,. part of the command in the script in the bcftools merge call only if params.filter_pass is true.
In other words, the script would be executed like this, if params.filter_pass is true (other lines removed for clarity):
bcftools merge \
-l vcflist \
-m none \
-f PASS,. \
--threads ${task.cpus} \
-O z \
-o assembled.vcf.gz
and if it instead params.filter_pass is false:
bcftools merge \
-l vcflist \
-m none \
--threads ${task.cpus} \
-O z \
-o assembled.vcf.gz
I know I can use conditional scripts but that would mean replicating the whole script stanza just to change one parameter.
Is this use case possible with Nextflow?

Answer 1

The general pattern is to use a local variable in the 'script' block and a ternary operator to add the -f PASS,. filter option when params.filter_pass is true:
process concatenate_vcf {
...
script:
def filter_pass = params.filter_pass ? '-f PASS,.' : ''
"""
echo "${vcf_files.join('\n')}" > vcf.list
bcftools merge \\
-l vcf.list \\
-m none \\
${filter_pass} \\
--threads ${task.cpus} \\
-O z \\
-o assembled.vcf.gz
"""
}
An if/else statement could also be used in place of the ternary operator if preferred.