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suggested reorder of list of script contents
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bobturneruk committed Mar 22, 2024
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11 changes: 4 additions & 7 deletions episodes/01-getting-started-with-nextflow.md
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Expand Up @@ -244,19 +244,16 @@ This is a Nextflow script, which contains the following:

1. An optional interpreter directive ("Shebang") line, specifying the location of the Nextflow interpreter.
2. `nextflow.enable.dsl=2` to enable DSL2 syntax.
3. A multi-line Nextflow comment, written using C style block comments, followed by a single line comment.
3. A multi-line Nextflow comment, written using C style block comments, there are more comments later in the file.
4. 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.
5. An unnamed `workflow` execution block, which is the default workflow to run.
6. A Nextflow channel used to read in data to the workflow.
5. A Nextflow channel `input_ch` used to read in data to the workflow.
6. An unnamed `workflow` execution block, which is the default workflow to run.
7. A call to the process `NUM_LINES`.
8. 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`.
12. A Nextflow channel `input_ch` used to read in data to the workflow.
13. An unnamed `workflow` execution block, which is the default workflow to run.
14. A call to the process `NUM_LINES` with input channel `input_ch`.
15. An operation on the process output, using the channel operator `.view()`.

## Running Nextflow scripts

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