Merge pull request #1 from biosustain/small_improvements

Small_improvements

.gitignore

@@ -2,3 +2,14 @@ _build
 *.docx
 .nextflow-console.log
 .nextflow.pid
+
+# ignore logs
+*.nextflow.log*
+ # Ignore the .nextflow directory created by Nextflow
+.nextflow
+work
+# Ignore the training directory cloned
+training
+# ignore results and data folder
+data
+results

course_contents/RunningRealWorkflow.md

@@ -15,7 +15,7 @@ To be able to run this pipeline we will clone the training repository from Nextf
 
 First cloning with `git clone`:
 ```bash
-git clone https://github.com/nextflow-io/training.git
+git clone https://github.com/nextflow-io/training.git --depth 1
 ```
 And then move to `training/nf-training`:
 ```bash
@@ -58,4 +58,4 @@ Let's run again the workflow by calling our config file:
 sudo nextflow run script7.nf -c course.config
 ```
 
- You are are welcome to have a look to the file that was downloaded `nextflow.config`, to see what usually these files contain and realise how important they are to setup the environment for the nextflow runs. The config file `nextflow.config` must be in the same folder where you are running your main script (`main.nf`) otherwise you need to specify the location with `-c`
+You are are welcome to have a look to the file that was downloaded `nextflow.config`, to see what usually these files contain and realise how important they are to setup the environment for the nextflow runs. The config file `nextflow.config` must be in the same folder where you are running your main script (`main.nf`) otherwise you need to specify the location with `-c`

course_contents/Tutorial.md

@@ -281,19 +281,16 @@ Workflows typically run on batches of inputs that are meant to be processed in b
 
 There are different factory channels to create the channels. Here you have an example where I used factory `Channel.fromFilePairs()` fastq read files.
 
-> params.reads = "$projectDir/data/*_{1,2}.fq.gz"
->
-> Channel
-
->        .fromFilePairs(params.reads, checkIfExists: true)
-
->        .toSortedList( { a, b -> a[0] <=> b[0] } )
-
->        .flatMap()
-
->        .set { read_pairs_ch }
-
->        read_pairs_ch.view()
+```groovy
+params.reads = "$projectDir/data/*_{1,2}.fq.gz"
+
+Channel
+    .fromFilePairs(params.reads, checkIfExists: true)
+    .toSortedList( { a, b -> a[0] <=> b[0] } )
+    .flatMap()
+    .set { read_pairs_ch }
+    read_pairs_ch.view()
+```
 
 `.toSortedList`, `.flatMap`, `.set`, `.view` are operators to transform the channel and achieve the input files in the desired format.