Syntax quirk when creating scripts

Training
1

I am working through the hello-nextflow tutorial, messing around with processes to understand what is happening with channels. I have created a process with the following script:

cat $(ls) > “collected_results.txt”

I know this is valid bash syntax to list the contents of every file identified by ls. However, in the .command.sh, this is being converted to cat ls) > “collected_results.txt". Why is the opening parenthesis being removed? The process runs as expected when I replace $(ls) with `ls`.

2

Hi, sorry I missed your question. I figured this had something to do with how Nextflow interprets the $ for variable substitution but wasn’t sure exactly what the syntax rules are, so I checked with Seqera AI and got this. It doesn’t seem to be able to explain the missing parenthesis, so I’ll ask internally to see if anyone has an answer on that specific point, but hopefully this clarifies the syntax rules and behavior at least.

The Issue: Nextflow Variable Interpolation

The problem you’re experiencing is related to how Nextflow handles variable interpolation in script strings. Here’s what’s happening:

Why $(ls) becomes ls)

When you use double-quoted strings (""") in Nextflow scripts, Nextflow treats anything starting with $ as a potential Nextflow variable that needs to be interpolated.

In your case:

  • $(ls) is being interpreted as $ followed by (ls)

  • Nextflow tries to find a variable named (ls) (which doesn’t exist)

  • Since the variable doesn’t exist, Nextflow removes the $ but keeps the rest: (ls)

  • This results in the malformed cat ls) > "collected_results.txt"

Why Backticks Work

When you use backticks `ls`, this is not interpreted as a Nextflow variable because:

  • Nextflow only looks for $variableName or ${variableName} patterns

  • Backticks are treated as literal bash syntax and passed through unchanged

Solutions

Here are several ways to fix this:

1. Escape the Dollar Sign (Recommended)

script:
"""
cat \$(ls) > "collected_results.txt"
"""

2. Use Single Quotes (If no Nextflow variables needed)

script:
'''
cat $(ls) > "collected_results.txt"
'''

3. Continue Using Backticks

script:
"""
cat `ls` > "collected_results.txt"
"""

4. Use the Shell Section (Alternative approach)

shell:
'''
cat $(ls) > "collected_results.txt"
'''

Key Takeaway

From the Nextflow documentation:

Since Nextflow uses the same Bash syntax for variable substitutions in strings, you must manage them carefully depending on whether you want to evaluate a Nextflow variable or a Bash variable.

When using double-quoted strings in Nextflow:

  • $variable → Nextflow variable interpolation

  • \$variable → Bash variable (escaped)

  • $(command) → Nextflow tries to interpolate $(command) as a variable

  • \$(command) → Bash command substitution (escaped)

The escaped version (\$(ls)) is the most appropriate solution for your use case since it preserves the intended bash command substitution while preventing Nextflow from trying to interpolate it as a variable.