From f8b755d1349583e5255f11966a84dc683b202b58 Mon Sep 17 00:00:00 2001
From: Erik Fasterius <erik.fasterius@outlook.com>
Date: Fri, 18 Mar 2022 12:51:54 +0100
Subject: [PATCH] Add pipeline parameters section

---
 _episodes/01-getting-started-with-nextflow.md | 88 ++++++++++++++++++-
 1 file changed, 87 insertions(+), 1 deletion(-)

diff --git a/_episodes/01-getting-started-with-nextflow.md b/_episodes/01-getting-started-with-nextflow.md
index 9545fad3..21013183 100644
--- a/_episodes/01-getting-started-with-nextflow.md
+++ b/_episodes/01-getting-started-with-nextflow.md
@@ -264,7 +264,7 @@ To run a Nextflow script use the command `nextflow run <script_name>`.
 > > You should see output similar to the text shown below:
 > >
 > > ~~~
-> > N E X T F L O W  ~  version 20.10.0
+> > N E X T F L O W  ~  version 21.04.3
 > > Launching `word_count.nf` [fervent_babbage] - revision: c54a707593
 > > executor >  local (1)
 > > [21/b259be] process > NUM_LINES (1) [100%] 1 of 1 ✔
@@ -281,4 +281,90 @@ To run a Nextflow script use the command `nextflow run <script_name>`.
 > {: .solution}
 {: .challenge}
 
+## Pipeline parameters
+
+The Nextflow `word_count.nf` script defines a pipeline parameter
+`params.input`. Pipeline parameters enable you to change the input to the
+workflow at runtime, via the command line or a configuration file, so they are
+not hard-coded into the script.
+
+Pipeline parameters are declared in the workflow by prepending the prefix
+`params`, separated by dot character, to a variable name e.g., `params.input`.
+Their value can be specified on the command line by prefixing the parameter
+name with a double dash character, e.g., `--input`.
+
+We can also use wild cards to specify multiple input files. In the example
+below we use the `*` to match any sequence of characters with `.fastq.gz`. Note
+that if you use wild card characters on the command line you must enclose the
+value in quotes.
+
+Re-run the Nextflow script by entering the following command in your terminal:
+
+~~~
+nextflow run word_count.nf --input 'data/untrimmed_fastq/*.fastq.gz'
+~~~~
+{: .language-bash}
+
+~~~
+N E X T F L O W  ~  version 21.04.3
+Launching `word_count.nf` [desperate_agnesi] - revision: bf77afb9d7
+executor >  local (6)
+[60/584db8] process > NUM_LINES (5) [100%] 6 of 6 ✔
+SRR2589044_1.fastq.gz 4428360
+SRR2589044_2.fastq.gz 4428360
+SRR2584863_1.fastq.gz 6213036
+SRR2584863_2.fastq.gz 6213036
+SRR2584866_2.fastq.gz 11073592
+SRR2584866_1.fastq.gz 11073592
+~~~~
+{: .output}
+
+The pipeline executes the process 6 times; one process for each file matching
+the string. Since each process is executed in parallel, there is no guarantee
+of which output is reported first. When you run this script, you may see the
+process output in a different order.
+
+Nextflow stores intermediate files in a `work` sub-directory in your current
+directory, which might look like this:
+
+~~~
+work/
+├── 13
+│   └── 46936e3927b74ea6e5555ce7b7b56a
+│       └── SRR2589044_2.fastq.gz -> nextflow_tutorial/data/untrimmed_fastq/SRR2589044_2.fastq.gz
+├── 43
+│   └── 3819a4bc046dd7dc528de8eae1c6b8
+│       └── SRR2584863_1.fastq.gz -> nextflow_tutorial/data/untrimmed_fastq/SRR2584863_1.fastq.gz
+├── 5a
+│   └── d446a792db2781ccd0c7aaafdff329
+│       └── SRR2584866_2.fastq.gz -> nextflow_tutorial/data/untrimmed_fastq/SRR2584866_2.fastq.gz
+├── 76
+│   └── b1e11f2e706b901e0c57768a2af59f
+│       └── SRR2589044_1.fastq.gz -> nextflow_tutorial/data/untrimmed_fastq/SRR2589044_1.fastq.gz
+├── 9c
+│   └── 1b1ebc2ea11a395e4e9dcf805b2c7d
+│       └── SRR2584863_2.fastq.gz -> nextflow_tutorial/data/untrimmed_fastq/SRR2584863_2.fastq.gz
+└── ce
+    └── b94ef609ee54f4b7ea79dc23eb32bb
+        └── SRR2584866_1.fastq.gz -> nextflow_tutorial/data/untrimmed_fastq/SRR2584866_1.fastq.gz
+
+12 directories, 6 files
+~~~~
+{: .output}
+
+Nextflow has a log command to display the logs of all previous executions. Type
+the following on the command line to display an output similar as below:
+
+~~~
+nextflow log
+~~~~
+{: .language-bash}
+
+~~~
+TIMESTAMP               DURATION        RUN NAME                STATUS  REVISION ID     SESSION ID                              COMMAND
+2021-11-16 07:17:23     5.9s            irreverent_leakey       OK      bf77afb9d7      17d06cd0-3bb9-4d32-9d75-48bfdf5401a9    nextflow run word_count.nf
+2021-11-16 07:23:00     11.1s           desperate_agnesi        OK      bf77afb9d7      41f78242-27d7-462a-a88d-80b6ec9dc5db    nextflow run word_count.nf --input 'data/untrimmed_fastq/*.fastq.gz'
+~~~~
+{: .output}
+
 {% include links.md %}