carpentries-incubator / workflows-nextflow

Workflow management with Nextflow and nf-core
https://carpentries-incubator.github.io/workflows-nextflow/
Other
18 stars 29 forks source link

Reordering description of the 'First Script' description #104

Open louisegrimble opened 5 months ago

louisegrimble commented 5 months ago

The reordering and re-configuring allows for the learner to follow the script along with the description in a more appropriate, line by line- rather than searching through the description for the description line that matches the section of code. Removed some lines of code that were repeated.

Here is the revised text:

  1. An optional interpreter directive (“Shebang”) line, specifying the location of the Nextflow interpreter. 2.nextflow.enable.dsl=2to enable DSL2 syntax.
  2. A multi-line Nextflow comment, written using C style block comments, followed by a single line comment.
  3. A pipeline parameter params.input which is given a default value, of the relative path to the location of a compressed fastq file, as a string.
  4. An unnamed workflow execution block, which is the default workflow to run.
  5. A Nextflow channel used to read in data to the workflow.
  6. A call to the process NUM_LINES.
  7. An operation on the process output, using the channel operator .view().
  8. A Nextflow process block named NUM_LINES, which defines what the process does.
  9. An input definition block that assigns the input to the variable read, and declares that it should be interpreted as a file path.
  10. An output definition block that uses the Linux/Unix standard output stream stdout from the script block.
  11. A script block that contains the bash commands printf '${read}' and gunzip -c ${read} | wc -l.