add callouts, fix exercises, formatting

docs/part2/01_salmon_idx.md

@@ -62,6 +62,12 @@ It contains:
 * The empty `output:` block for us to define the output data for the process.
 * The `script:` block prefilled with the command that will be executed.
 
+!!! info 
+
+    The process [`script`](https://www.nextflow.io/docs/latest/process.html#script)
+    block is executed as a Bash script by default. In Part 2 of the workshop, we will
+    only be using Nextflow variables within the `script` block.
+
 Next, we will edit the `input` and `output` definitions to match the specific
 data and results for this process. In the `00_index.sh` script, the relevant
 information is:  
@@ -285,6 +291,13 @@ params.transcriptome_file = "$projectDir/data/ggal/transcriptome.fa"
 
     We will use [`$projectDir`](https://www.nextflow.io/docs/latest/script.html#configuration-implicit-variables) to indicates the directory of the `main.nf` script. This is defined by Nextflow as the directory where the `main.nf` script is located.
 
+!!! info "The `params` and `process` names do not need to match!"  
+
+    In the `INDEX` process, we defined the input as a path called `transcriptome`, whereas
+    the parameter is called `transcriptome_file`. These do not need to be identical names
+    as they are called in different scopes (the `INDEX` process scope, and `workflow` scope,
+    respectively).
+
 Recall that [parameters](https://www.nextflow.io/docs/latest/module.html#module-parameters)
 are inputs and options that can be customised when the workflow is 
 executed. They allow you to control things like file paths and options for 

docs/part2/02_fastqc.md

@@ -293,9 +293,9 @@ definition of `tuple val(sample_id), path(reads_1), path(reads_2)`:
 [gut, /home/setup2/hello-nextflow/part2/data/ggal/gut_1.fq, /home/setup2/hello-nextflow/part2/data/ggal/gut_2.fq]
 ```
 
-!!! quote "Checkpoint"  
+!!! quote "How's it going?"
 
-    Zoom react Y/N
+    Once you have run the workflow, select the  **"Yes"** react on Zoom.
 
 Next, we need to assign the channel we create to a variable so it can be passed to the `FASTQC`
 process. Assign to a variable called `reads_in`, and remove the `.view()`
@@ -363,45 +363,111 @@ executor >  local (1)
 If you inspect `results/fastqc_gut_logs` there is an `.html` and `.zip` file
 for each of the `.fastq` files.  
 
-> Need to revisit the Advanced exercise  
+!!! example "Advanced exercise"  
 
-??? example "Advanced exercise"  
+    This advanced exercise walks through inspecing the output of the intermediate
+    operators in the `reads_in` channel:  
 
-    Inspect what the `.fromPath()` and `.splitCsv()` commands do by using `.view()`
+    - `Channel.fromPath`
+    - `.splitCsv`
 
+    The current workflow block should look like:
+
     ```groovy title="main.nf"
+    // Define the workflow  
     workflow {
-        Channel
-            .fromPath(params.reads)
-            .view()
-
-        index_ch = INDEX(params.transcriptome_file)
-    ```
-
-    ```console title="Output"
-    Launching `main.nf` [hungry_lalande] DSL2 - revision: 587b5b70d1
 
-    [de/fef8c4] INDEX [100%] 1 of 1, cached: 1 ✔
-    /home/setup2/hello-nextflow/part2/data/samplesheet.csv
+        // Run the index step with the transcriptome parameter
+        INDEX(params.transcriptome_file)
 
-    ```
-
-    ```groovy title="main.nf"
-    workflow {
-        Channel
-            .fromPath(params.reads)
+        // Define the fastqc input channel
+        reads_in = Channel.fromPath(params.reads)
             .splitCsv(header: true)
-            .view()
+            .map { row -> [row.sample, file(row.fastq_1), file(row.fastq_2)] }
 
-        index_ch = INDEX(params.transcriptome_file)
+        // Run the fastqc step with the reads_in channel
+        FASTQC(reads_in)
+    }
     ```
+
+    **`Channel.fromPath`**  
+
+    1. In the workflow scope, comment out the lines for `.splitCsv`, `.map`, and `FASTQC()`
+    2. Add `.view()` on the line after `Channel.fromPath` and before the commented `.splitCsv`
+    3. Run the workflow with `-resume`  
+
+    ??? note "Solution"
+
+        ```groovy title="main.nf" hl_lines="9-11 14"
+        // Define the workflow  
+        workflow {
+        
+            // Run the index step with the transcriptome parameter
+            INDEX(params.transcriptome_file)
+        
+            // Define the fastqc input channel
+            reads_in = Channel.fromPath(params.reads)
+                .view()
+                //.splitCsv(header: true)
+                //.map { row -> [row.sample, file(row.fastq_1), file(row.fastq_2)] }
+        
+            // Run the fastqc step with the reads_in channel
+            //FASTQC(reads_in)
+
+        }
+        ```
+        
+        The output of the `Channel.fromPath(params.reads)` step produces a path to the samplesheet:  
+
+        ```console title="Output"
+        Launching `main.nf` [hungry_lalande] DSL2 - revision: 587b5b70d1
+        
+        [de/fef8c4] INDEX [100%] 1 of 1, cached: 1 ✔
+        /home/user1/part2/data/samplesheet.csv
+        
+        ```
+
+    **`.splitCsv`**  
+
+    1. In the workflow scope, *un*comment the line for `.splitCsv`
+    2. Move `.view()` to the line after `.splitCsv` (before the commented `.map` line)
+    3. Run the workflow with `-resume`  
 
-    ```console title="Output"
-    Launching `main.nf` [tiny_yonath] DSL2 - revision: 22c2c9d28f
-    [de/fef8c4] INDEX | 1 of 1, cached: 1 ✔
-    [sample:gut, fastq_1:data/ggal/gut_1.fq, fastq_2:data/ggal/gut_2.fq]
-
-    ```
+    ??? note "Solution"
+
+        ```groovy title="main.nf" hl_lines="9-10"
+        // Define the workflow  
+        workflow {
+        
+            // Run the index step with the transcriptome parameter
+            INDEX(params.transcriptome_file)
+        
+            // Define the fastqc input channel
+            reads_in = Channel.fromPath(params.reads)
+                .splitCsv(header: true)
+                .view()
+                //.map { row -> [row.sample, file(row.fastq_1), file(row.fastq_2)] }
+        
+            // Run the fastqc step with the reads_in channel
+            //FASTQC(reads_in)
+
+        }
+        ```
+
+        `.splitCsv` takes the path from `.fromPath` and reads the header and data line as a tuple.
+        Each element in the tuple is named by the header in the correspoding column in the samplesheet:
+
+        ```console title="Output"
+        Launching `main.nf` [tiny_yonath] DSL2 - revision: 22c2c9d28f
+        [de/fef8c4] INDEX | 1 of 1, cached: 1 ✔
+        [sample:gut, fastq_1:data/ggal/gut_1.fq, fastq_2:data/ggal/gut_2.fq]
+        
+        ```
+
+        The `.map` step takes that tuple and formats it into the tuple that is emitted by `reads_in`.
+
+    Before proceeding, ensure to *un*comment the `.map` and `FASTQC` lines, and remove `.view()`.
+
 
 !!! abstract "Summary"
 

docs/part2/03_quant.md

@@ -189,6 +189,10 @@ process QUANTIFICATION {
 
 You have just defined a process with multiple inputs!  
 
+!!! quote "How's it going?"
+
+    Once you have defined the `process` block, select the  **"Yes"** react on Zoom.
+
 ### 5. Call the process in the `workflow` scope  
 
 Recall that the inputs for the `QUANTIFICATION` process are emitted by the