Added RunningRealWorflow and SeqeraPlatform markdowns

course_contents/RunningRealWorkflow.md

@@ -0,0 +1,18 @@
+# RNA-Seq workflow
+
+Let's run a commonly used Nextflow pipeline to analise RNA-seq data ([nf-core/rnaseq](https://nf-co.re/rnaseq/3.17.0)).
+
+This pipeline that we will run will cover the following 4 steps using diffrent coomonly used bioinformatics tools:
+
+1. Indexes a transcriptome file
+2. Quality control of the high throughput sequence data with **FastQC**
+3. Quantification  of transcripts using **Salmon**
+4. Creates a **MultiQC** report. MultiQC searches a given directory for analysis logs and compiles a easy-viwing HTML report.
+
+This is based on this part of [Nextflow tutorial](https://training.nextflow.io/basic_training/rnaseq_pipeline/). There you can find the pipeline broken into the different pieces in a collection of 7 different scripts if you want to get into the details.
+
+In this part of the tutorial you can also see that Nextflow allows the execution of a workflow project directly from a GitHub repository. This [GitHub repository](https://github.com/nextflow-io/rnaseq-nf) hosts a version of this tutorial workflow (first 4 steps with some test data). You can run it specifying the project name and executing each process in a Docker container (`with-docker` as parameter). The containers will be automatically downloaded and saved in the folder `$HOME/.nextflow`.
+
+```groovy
+nextflow run nextflow-io/rnaseq-nf -with-docker
+```

course_contents/SeqeraPlatform

@@ -0,0 +1,26 @@
+# Run Nextflow CLI with Seqera Platform visualizing and capturing logs
+
+## Seqera platform
+
+The Seqera Platform is a collaborative environment where pipelines and analysis results can be launched, cataloged, monitored, organized, and shared with colleagues.
+
+Seqera platform can help us by:
+
+1. giving researchers early access to pipelines and computational resources
+2. promoting effective collaboration, 
+3. standardizing and accelerating the generation of results, 
+4. ensuring compliance and security providing the framework for reliable and reproducible pipeline execution 
+5. allowing us to optimize and reduce computing and storage costs
+
+First you need to create an account and creat an access token. Later you need to export the token to your system:
+
+```bash
+export TOWER_ACCESS_TOKEN=copyandpastetokenfromtheSqeraPlatformhere
+```
+
+Lets's run our first nextflow script in Seqera with the addition of the -with-tower command:
+
+```{code-block} groovy
+:caption: hello.nf capturing logs in Seqera platform
+nextflow run hello.nf -with-tower
+```

course_contents/Tutorial.md

@@ -16,10 +16,10 @@ nextflow -h
 ```
 ## Running our first script
 
-Let's run our first script, 'Hello World!' script. Open a new file in VSCode in the codespace and copy paste the following code. Save it as hello-world.nf.
+Let's run our first script, 'Hello World!' script. Open a new file in VSCode in the codespace and copy paste the following code. Save it as hello.nf.
 
 ```{code-block} groovy
-:caption: hello-world.nf
+:caption: hello.nf
 
 #!/usr/bin/env nextflow
 
@@ -52,8 +52,8 @@ As you can see, a Nextflow script involves two main types of core components: pr
 
 Let's try to run this code in your codespace:
 ```{code-block} groovy
-:caption: Running hello-world.nf
-nextflow run hello-world.nf
+:caption: Running hello.nf
+nextflow run hello.nf
 ```
 
 ## Find the output and logs in the work directory
@@ -89,7 +89,7 @@ output:
 
 Run the pipeline again!
 ```groovy
-nextflow run hello-world.nf
+nextflow run hello.nf
 ```
 Find the output file in the work directory.
 
@@ -105,7 +105,7 @@ process sayHello {
 
 Run the pipeline again!
 ```groovy
-nextflow run hello-world.nf
+nextflow run hello.nf
 ```
 Was the output file saved in there? Is it the same or different than the output file saved in the corresponding work directory?
 
@@ -171,7 +171,7 @@ sayHello(greeting_ch)
 And run the pipeline again!
 
 ```groovy
-nextflow run hello-world.nf
+nextflow run hello.nf
 ```
 
 ## Relaunch a pipeline without repeating steps
@@ -180,7 +180,7 @@ A very useful option of nextflow is the -resume to launch a pipeline again witho
 
 Run the workflow again with -resume
 ```groovy
-nextflow run hello-world.nf -resume
+nextflow run hello.nf -resume
 ```
 
 ## Use command line interface (CLI) parameters for inputs
@@ -195,7 +195,7 @@ greeting_ch = Channel.of(params.greeting)
 Run the pipeline! Let's greet på Dansk!
 
 ```groovy
-nextflow run hello-world.nf --greeting 'Hej verden!'
+nextflow run hello.nf --greeting 'Hej verden!'
 ```
 
 > Notice one thing here, for parameters that apply to a pipeline, we use a double hyphen (--), 
@@ -251,7 +251,7 @@ workflow {
 Let's greet på Dansk igen!
 
 ```groovy
-nextflow run hello-world.nf --greeting 'Hej verden!'
+nextflow run hello.nf --greeting 'Hej verden!'
 ```
 
 ## Let's run the script on a batch of input values
@@ -288,7 +288,7 @@ process sayHello {
 Let's run the script again. But hang on, to expand the logging to display one line per process call to have a closer look to what is going on, just add `-ansi-log false` to the command.
 
 ```groovy
-nextflow run hello-world.nf -ansi-log false
+nextflow run hello.nf -ansi-log false
 ```
 
 Check the results folder and the output files:
@@ -336,7 +336,7 @@ greeting_ch = Channel.fromPath(params.input_file)
 Ok, lets try this script one last time!
 
 ```groovy
-nextflow run hello-world.nf
+nextflow run hello.nf
 ```
 
 >You know how to provide the input values to the workflow via a file.
@@ -348,7 +348,7 @@ nextflow run hello-world.nf
 Here you have you first nextflow script in full! Congratulations!
 
 ```{code-block} groovy
-:caption: hello-world.nf
+:caption: hello.nf
 #!/usr/bin/env nextflow
 
 /*
@@ -410,12 +410,3 @@ workflow {
     convertToUpper(sayHello.out)
 }
 ```
-
-## Run Nextflow CLI with Seqera Platform visualizing and capturing logs
-
-Run a Nextflow workflow with the addition of the -with-tower command:
-
-```{code-block} groovy
-:caption: hello.nf capturing logs in Seqera platform
-nextflow run nextflow-io/hello -with-tower
-```

index.md

@@ -38,6 +38,8 @@ course_information/Timing
 
 course_contents/Contents
 course_contents/Tutorial
+course_contents/RunningRealWorkflow
+course_contents/SeqeraPlatform
 ```
 
 ```{toctree}