.trim() removed to keep new lines between collected versions

[SofiaDrobysheva]

On the page with 20.04 release highlights, in the Collecting version subsection, within an example code snippet, .trim() was removed to keep newline between recorded versions.

old:

workflow {
  Channel.topic('versions') 
    | unique()
    | map { process, name, version ->
      """
      ${process.tokenize(':').last()}:
        ${name}: ${version}
      """.stripIndent().trim()
    }
    | collectFile(name: 'collated_versions.yml')
    | CUSTOM_DUMPSOFTWAREVERSIONS
}

new:

workflow {
  Channel.topic('versions') 
    | unique()
    | map { process, name, version ->
      """\
      ${process.tokenize(':').last()}:
        ${name}: ${version}
      """.stripIndent()
    }
    | collectFile(name: 'collated_versions.yml')
    | CUSTOM_DUMPSOFTWAREVERSIONS
}

Output file example after .trim() is removed:

PREPROCESSING:
  cutadapt: 4.7
PREPROCESSING:
  ribodetector: 0.3.1
GET_SAMPLE_INFO:
  scd: 1.4.22

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[ewels]

Thanks!

[ewels]

I don't think that we need this do we?

[ewels]

Or rather, I should ask: was it intentional to add this and if so why?

[SofiaDrobysheva]

You are right, we do not necessarily need the backslash here!
What it does is that it prevent Groovy from inserting a newline immediately after opening the triple quotes.

So this would be the output with the backslash:

PREPROCESSING:
  cutadapt: 4.7
PREPROCESSING:
  ribodetector: 0.3.1
GET_SAMPLE_INFO:
  scd: 1.4.22

... and this would be the output without the backslash:

PREPROCESSING:
  ribodetector: 0.3.1

PREPROCESSING:
  cutadapt: 4.7

GET_SAMPLE_INFO:
  scd: 1.4.22

Saw the backslash in Ben Sherman's slack reply, though it was cool way of removing extra newlines :) But the pipeline would run either way, so the backslash in this case is a preference thing, I guess.

[SofiaDrobysheva]

Ben also mentioned .leftTrim(), this would be the output (looks the same way as when adding the backslash):

PREPROCESSING:
  cutadapt: 4.7
PREPROCESSING:
  ribodetector: 0.3.1
GET_SAMPLE_INFO:
  scd: 1.4.22

[ewels]

Ah ok great, let's leave it in then! I was worried that it would kill the newline and break the yaml, but if it's double spaced already then that's perfect.

Thanks for the explanation! 🙌🏻

[ewels]

Thanks!