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:
An optional interpreter directive (“Shebang”) line, specifying the location of the Nextflow interpreter.
2.nextflow.enable.dsl=2to enable DSL2 syntax.
A multi-line Nextflow comment, written using C style block comments, followed by a single line comment.
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.
An unnamed workflow execution block, which is the default workflow to run.
A Nextflow channel used to read in data to the workflow.
A call to the process NUM_LINES.
An operation on the process output, using the channel operator .view().
A Nextflow process block named NUM_LINES, which defines what the process does.
An input definition block that assigns the input to the variable read, and declares that it should be interpreted as a file path.
An output definition block that uses the Linux/Unix standard output stream stdout from the script block.
A script block that contains the bash commands printf '${read}' and gunzip -c ${read} | wc -l.
The reordering and re-configuring allows for the learner to follow the script along with the description in a more appropriate, line by line- rather than searching through the description for the description line that matches the section of code. Removed some lines of code that were repeated.
Here is the revised text:
nextflow.enable.dsl=2
to enable DSL2 syntax.params.input
which is given a default value, of the relative path to the location of a compressed fastq file, as a string.workflow
execution block, which is the default workflow to run.NUM_LINES
..view()
.NUM_LINES
, which defines what the process does.input
definition block that assigns the input to the variableread
, and declares that it should be interpreted as a file path.output
definition block that uses the Linux/Unix standard output streamstdout
from the script block.printf '${read}'
andgunzip -c ${read} | wc -l
.