TL;DR: Consider making your script a "third-party script", by making it executable and moving it into a folder called 'bin' in the root directory of your project repository. Nextflow automatically adds this folder to the $PATH in the execution environment and this would let you easily provide command-line arguments inside of a regular script block.
Typically, template files are used inside a script block with a shell script (e.g. BASH, ZSH) since:
The dollar character ($) is interpreted as a Nextflow variable
placeholder when the script is run as a Nextflow template, whereas it
is evaluated as a Bash variable when run as a Bash script. This can be
very useful to test your script autonomously, i.e. independently from
Nextflow execution. You only need to provide a Bash environment
variable for each the Nextflow variable existing in your script.
The advantage of template files is that you can test them independently of Nextflow. This is especially helpful if, for example, you already have a bunch of PBS (or SLURM) scripts (where you wouldn't usually provide command line arguments) and would like to use them as template files. For example:
Contents of templates/my_script.pbs:
#!/bin/bash
#PBS -N test_job
#PBS -q default_queue
#PBS -S /bin/bash
#PBS -l walltime=1:00:00
#PBS -l ncpus=1
#PBS -l mem=4gb
set -eu
echo "${greeting} world"
Contents of main.nf:
process test {
debug true
input:
val(greeting) from 'Hello', 'Hola', 'Bonjour'
script:
template 'my_script.pbs'
}
Results:
$ nextflow run main.nf
N E X T F L O W ~ version 22.04.4
Launching `main.nf` [backstabbing_meitner] DSL1 - revision: 5f66c981d2
executor > local (3)
[ba/93de8f] process > test (2) [100%] 3 of 3 ✔
Hello world
Bonjour world
Hola world
Note that you could also run the above PBS script using your bash interpreter (since it is basically just a regular shell script with some comments or comment lines at the top):
$ greeting="Hallo" bash templates/my_script.pbs
Hallo world
Or if, in your testing, you need the variable in subsequent commands, export it:
$ export greeting="Hallo"
$ bash templates/my_script.pbs
Hallo world
$ echo "${greeting} there"
Hallo there
Note that shell blocks also support the use of template files. This is useful when your script contains dollar variables that should not be Nextflow variable placeholders, for example:
Contents of templates/my_script.sh:
#!/bin/bash
set -eu
echo "!{greeting} world" | awk '{ print $1 }'
Contents of main.nf:
process test {
debug true
input:
val(greeting) from 'Hello', 'Hola', 'Bonjour'
shell:
template 'my_script.sh'
}
Results:
$ nextflow run main.nf
N E X T F L O W ~ version 22.04.4
Launching `main.nf` [tiny_dalembert] DSL1 - revision: 79aeea8b7e
executor > local (3)
[13/78be26] process > test (3) [100%] 3 of 3 ✔
Hola
Hello
Bonjour
However, shell scripts with exclamation marks (!) to denote variables have limited value outside of Nextflow in my opinion:
$ greeting="Hallo" bash templates/my_script.sh
!{greeting}
A better way might be to instead make your Python script a "third-party script". Just make it executable and move it into a folder called 'bin' in the root directory of your project repository. Nextflow automatically adds this folder to the $PATH in the execution environment. This lets you use it in a regular script block so that you can provide command-line arguments in the usual way:
Contents of bin/my_script.py:
#!/usr/bin/python
import sys
the_greeting = sys.argv[1]
print(f"{the_greeting} world")
Contents of main.nf:
process test {
debug true
input:
val(greeting) from 'Hello', 'Hola', 'Bonjour'
script:
"""
my_script.py "${greeting}"
"""
}
Results:
$ nextflow run main.nf
N E X T F L O W ~ version 22.04.4
Launching `main.nf` [backstabbing_banach] DSL1 - revision: 4937773725
executor > local (3)
[34/0df158] process > test (1) [100%] 3 of 3 ✔
Bonjour world
Hola world
Hello world
