Convert to Nextflow strict syntax

[Copilot]

Nextflow strict syntax requires explicit parentheses on all method calls. Two violations in main.nf prevented strict mode compilation.

Changes

• Channel.fromPath 'welcome.txt' → Channel.fromPath('welcome.txt')
• splitText | view → splitText() | view()

- SAYHELLOINSEVERALLANGUAGES(Channel.fromPath 'welcome.txt')
- SAYHELLOINSEVERALLANGUAGES.out | splitText | view
+ SAYHELLOINSEVERALLANGUAGES(Channel.fromPath('welcome.txt'))
+ SAYHELLOINSEVERALLANGUAGES.out | splitText() | view()

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• www.nextflow.io
  • Triggering command: /home/REDACTED/work/_temp/ghcca-node/node/bin/node /home/REDACTED/work/_temp/ghcca-node/node/bin/node --enable-source-maps /home/REDACTED/work/_temp/copilot-developer-action-main/dist/index.js (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

Can you convert this Nextflow script to the strict syntax defined here https://www.nextflow.io/docs/latest/reference/syntax.html#syntax-page?

The user has attached the following files from their workspace:

• main.nf

---

💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.