more process updates

_episodes/05-processes-part1.md

@@ -60,7 +60,7 @@ To add the process to a workflow add a `workflow` block, and call the process li
 **Note:** As we are using DSL2 we need to include `nextflow.enable.dsl=2` in the script.
 
 ~~~
-//process_index.nf
+// process/process_index.nf
 nextflow.enable.dsl=2
 
 process INDEX {
@@ -118,10 +118,10 @@ Tip: you can try to figure out what's wrong by changing to the process work dir
 
 What happened? Well, in our case we can't see the `salmon` executable; the error indicates it is not found. 
 
-How do we address this? There are a number of options, but the general 'best practice' way would be to use a __directive__ which loads the software into the environment when the script is run. For example, this could be done by using the `module` directive and the appropriate [environment module](https://modules.sourceforge.net):
+How do we address this? There are a number of options, but the general 'best practice' way would be to use a __directive__ which loads the software into the environment when the script is run. For example, this could be done by using the `module` directive and the appropriate [environment module](https://modules.sourceforge.net).  Below is a modified version of the script in `./process/process_index.nf` which includes such a directive:
 
 ~~~
-//process_index.nf
+
 nextflow.enable.dsl=2
 
 process INDEX {
@@ -244,8 +244,6 @@ For example:
 nextflow.enable.dsl=2
 
 process PROCESSBAM {
-    module "SAMtools/1.17-IGB-gcc-8.2.0"
-
     script:
     """
     samtools sort -o ref1.sorted.bam ${projectDir}/data/yeast/bams/ref1.bam
@@ -313,7 +311,7 @@ workflow {
 ~~~
 {: .language-groovy }
 
-This allows the use of a different programming languages which may better fit a particular job. However, for large chunks of code it is suggested to save them into separate files and invoke them from the process script.
+This allows the use of a different programming languages which may better fit a particular job. However, for large chunks of code it is suggested to save them into separate files and invoke them from the process script. 
 
 ~~~
 nextflow.enable.dsl=2
@@ -332,6 +330,8 @@ workflow {
 ~~~
 {: .language-groovy }
 
+Note that you will need to ensure any libraries are also loaded in if they are needed (e.g, Python libraries like `pandas`, or R libraries like `ggplot2`).
+
 > ## Associated scripts
 > Scripts such as the one in the example above, `myscript.py`, can be stored in a `bin` folder at the same directory level as the Nextflow workflow script that invokes them, and given execute permission. Nextflow will automatically add this folder to the `PATH` environment variable. To invoke the script in a Nextflow process, simply use its filename on its own rather than invoking the interpreter e.g. `myscript.py` instead of `python myscript.py`.
 {: .callout }