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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` diff --git a/_sources/course_contents/Tutorial.md b/_sources/course_contents/Tutorial.md index 4420f8f..fc3ab58 100644 --- a/_sources/course_contents/Tutorial.md +++ b/_sources/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. diff --git a/course_contents/RunningRealWorkflow.html b/course_contents/RunningRealWorkflow.html index 7153c93..5072026 100644 --- a/course_contents/RunningRealWorkflow.html +++ b/course_contents/RunningRealWorkflow.html @@ -343,7 +343,7 @@

RNA-Seq workflowNextflow tutorial. 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.

To be able to run this pipeline we will clone the training repository from Nextflow training materials in github. Here you can enjoy the hello training, their fundamentals training based on the rnaseq pipeline and the advanced training with all data, files and scripts needed.

First cloning with git clone:

-
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:

diff --git a/course_contents/Tutorial.html b/course_contents/Tutorial.html
index 261a4a7..794667d 100644
--- a/course_contents/Tutorial.html
+++ b/course_contents/Tutorial.html
@@ -617,35 +617,16 @@ 
Let’s run the script on a batch of input valuesWorkflows typically run on batches of inputs that are meant to be processed in bulk, so we want to upgrade the workflow to accept multiple input values.

 
Channel.of() factory we’ve been using is quite happy to accept more than one value. Imagine that these could be used to pass a list of genes, genomes or files …

 
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()
+
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.

 
Back into our channel. Please modify the following, where do you need to add that?

 
// create a channel for inputs
diff --git a/searchindex.js b/searchindex.js
index d323d9a..f284baa 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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