Update workflows to DSL2

[bentsherman]

Resolves #23

This PR updates all workflow patterns to DSL2.

Notes:

• I kept the channel duplication pattern just to show that into is no longer needed in DSL2
• Renamed "mock dependency" to "state dependency" for clarity, "mock" suggests something related to unit testing or dry run
• I tended to use syntax shortcuts like | and & as much as possible, let me know if I went overboard or could do more in any examples

TODO:

• [x] Update docs files with new examples

[pditommaso]

This is great! however I've tried a couple and there are not working. e.g

process foo {
  errorStrategy 'ignore'
  script:
  '''
  echo This is going to fail!
  exit 1
  '''
}

process bar {
  script:
  '''
  echo OK
  '''
}

workflow {
  foo & bar
}

and

process foo {
  publishDir 'results', saveAs: { filename -> filename.endsWith(".zip") ? "zips/$filename" : filename }

  output:
  path '*'

  '''
  touch this.txt
  touch that.zip
  '''
}

workflow {
  foo
}

Broken docs is much worse than not having docs. Those should be tested one by one before merging.

[bentsherman]

Okay it looks like I was misunderstanding the DSL2 syntax here. I assumed that

workflow {
  foo
}

would simply call foo, but it looks like you have to explicitly invoke foo(), and foo by itself is only valid when using pipes. I will review and correct my changes accordingly.

[bentsherman]

The reason I didn't catch these problems is because the syntax is still valid, the workflow doesn't fail but simply runs nothing and exits. Might warrant some clarification in the Nextflow docs.

For example, consider these examples:

// runs foo and then bar
workflow {
  foo | bar
}

// does nothing
workflow {
  foo
}

// does nothing
workflow {
  foo & bar
}

[bentsherman]

Okay I made the changes you requested 👍

[pditommaso]

This is wrong

process foo {
  echo true
  input:
  file x

  script:
  """
  echo your_command --input $x
  """
}

workflow {
  foo("$baseDir/data/reads/*_1.fq.gz")
}

because the input is declared as file and the concrete input is a string therefore the process will convert the path string into a file :/

think it's a good opportunity to change all file to path in the input and output definitions

[bentsherman]

You got it. Only exception is process-per-file-chunk.nf, because it uses behavior of file to convert implicitly text into file chunks. If you're trying to get away from that pattern, you can use the split command instead like I do here.

One other question is, do you want to replace echo with debug ? It will remove the deprecation warning but then it won't work with Nextflow < 22.04.

[pditommaso]

You got it. Only exception is process-per-file-chunk.nf, because it uses behavior of file to convert implicitly text into file chunks

Ok, that's fine to keep it as example why to use file instead of path 👍

One other question is, do you want to replace echo with debug

Yes, let's go with debug!

[bentsherman]

Ready to go 👍

[pditommaso]

¡Vamos!