Textual updates

Author: KrisDavie

docs/nextflow/configs.md

@@ -186,7 +186,7 @@ params {
 ## Extra exercises
 
 ````{tab} Extra exercise 1
-Complete the `nextflow.config` and `params.config` files in the 'exercises/04_configs/' folder. These config files should accompany the script `exercises/04_configs/RNAseq.nf`. The commmand to run this pipeline should be: `nextflow run exercises/04_configs/RNAseq.nf -profile docker`. 
+Complete the `nextflow.config` and `params.config` files in the `exercises/04_configs/` folder. These config files should accompany the script `exercises/04_configs/RNAseq.nf`. The commmand to run this pipeline should be: `nextflow run exercises/04_configs/RNAseq.nf -profile docker`. 
 ```` 
 ````{tab} Solution 1
 The solution is available in the `exercises/04_configs/solutions/` folder. 

docs/nextflow/project.md

@@ -1,6 +1,6 @@
 # Project
 
-For day two, each of you will build a small-scale metagenomics pipeline from scratch to test out what you’ve learned so far.
+For the second half of day two, each of you will build a small-scale metagenomics pipeline from scratch to test out what you’ve learned so far.
 
 ## Concept
 
@@ -20,7 +20,7 @@ Before you start the project, make sure to `cd` to the `project` directory and w
 
 For this project, we will use data from *[Vandeputte et al. (2017)](https://www.nature.com/articles/nature24460)*: a well-known study from the VIB centre for microbiology that was published in Nature. This study took faecal samples from 135 participants to examine their gut microbiota.
 
-To keep computation times to a minimum, we will work with a few subsets from this data. You can pull in this data by running the `get_project_data.sh` script that has been provided for you.
+To keep computation times to a minimum, we will work with a two subsets of this data. You can download this data by running the `get_project_data.sh` script that has been provided for you.
 
 ```bash
 bash get_project_data.sh
@@ -39,6 +39,14 @@ Set up a `main.nf` script in which you will build your pipeline that uses nextfl
 
 All the docker containers we will need are already publicly available, so don’t worry about having to write Dockerfiles yourself 🙂
 
+```{note}
+The following docker containers will work well with Nextflow for the pipeline you're going to create:
+  - fastqc: `biocontainers/fastqc:v0.11.9_cv8` 
+  - DADA2: `blekhmanlab/dada2:1.26.0` 
+  - Python: `python:slim-bullseye` 
+  - Cutadapt: `kfdrc/cutadapt:latest` 
+```
+
 ### Step 1: Quality Control
 
 After pulling in and setting up the data, we’re first interested in examining the quality of the sequencing data we got. 

docs/nextflow/reports.md

@@ -24,7 +24,17 @@ Nextflow has an embedded function for reporting a various information about the
     As of Nextflow 22.04, the DAG can also be output in mermaid format, more information can be found [here](https://www.nextflow.io/docs/latest/tracing.html#dag-visualisation).
     ```
 
-3. **Tower**
+3. **Timeline Report**
+
+    After running the nextflow pipeline script with the option `-with-timeline`, find the html report in the folder from where you launched the pipeline. 
+
+    ```bash
+    nextflow run exercises/05_reports/RNAseq.nf -with-timeline -profile docker
+    ```
+    
+    This report summarizes the execution time of each process in your pipeline. It can be used to identify bottlenecks and to optimize the pipeline. More information about the formt of the timeline report can be found [here](https://www.nextflow.io/docs/latest/tracing.html#timeline-report).
+
+4. **Tower**
 
     Adding the parameter `-with-tower` enables the Seqera Tower service and will output the reports to a browser-based platform. More about Tower below.
 

project/project-solutions/modules/reads2counts.nf

@@ -2,7 +2,7 @@
 
 process DADA2 {
     // DIRECTIVES: set the docker container, the directory to output to, and the amount of cpus to allocate to this process
-    container 'golob/dada2:1.14.1.ub.1804'
+    container 'blekhmanlab/dada2:1.26.0'
     publishDir "${params.outdir}/dada2", mode: 'copy', overwrite: true
     cpus 4
 

project/project-solutions/modules/rev_comp.nf

@@ -3,7 +3,7 @@
 params.fw_primer = "GTGCCAGCMGCCGCGGTAA"
 
 process REVERSE_COMP {
-    container 'rackspacedot/python37'
+    container 'python:slim-bullseye'
     //container 'julia'
     //container 'r-base'
     //container 'debian'