Merge branch 'main' into ggrimes-patch-1

.github/workflows/README.md

@@ -2,7 +2,7 @@
 
 This directory contains workflows to be used for Lessons using the {sandpaper}
 lesson infrastructure. Two of these workflows require R (`sandpaper-main.yaml`
-and `pr-recieve.yaml`) and the rest are bots to handle pull request management.
+and `pr-receive.yaml`) and the rest are bots to handle pull request management.
 
 These workflows will likely change as {sandpaper} evolves, so it is important to
 keep them up-to-date. To do this in your lesson you can do the following in your
@@ -94,7 +94,7 @@ branch called `update/workflows` and a pull request is created. Maintainers are
 encouraged to review the changes and accept the pull request if the outputs
 are okay.
 
-This update is run ~~weekly or~~ on demand.
+This update is run weekly or on demand.
 
 ### 03 Maintain: Update Package Cache (update-cache.yaml)
 
@@ -140,7 +140,7 @@ Once the checks are finished, a comment is issued to the pull request, which
 will allow maintainers to determine if it is safe to run the 
 "Receive Pull Request" workflow from new contributors.
 
-### Recieve Pull Request (pr-recieve.yaml)
+### Receive Pull Request (pr-receive.yaml)
 
 **Note of caution:** This workflow runs arbitrary code by anyone who creates a
 pull request. GitHub has safeguarded the token used in this workflow to have no
@@ -171,7 +171,7 @@ The artifacts produced are used by the next workflow.
 
 ### Comment on Pull Request (pr-comment.yaml)
 
-This workflow is triggered if the `pr-recieve.yaml` workflow is successful.
+This workflow is triggered if the `pr-receive.yaml` workflow is successful.
 The steps in this workflow are:
 
 1. Test if the workflow is valid and comment the validity of the workflow to the

.github/workflows/sandpaper-version.txt

@@ -1 +1 @@
-0.14.1.9000
+0.16.5

CITATION.cff

@@ -0,0 +1,16 @@
+cff-version: 1.2.0
+message: "If you use this dataset, please cite it using the following metadata."
+authors:
+  - family-names: Grimes
+    given-names: Graeme
+title: "RNA-seq training dataset"
+version: "1.0"
+doi: 10.6084/m9.figshare.14822481
+date-released: 2021-06-22
+url: https://figshare.com/articles/dataset/RNA-seq_training_dataset/14822481
+keywords:
+  - RNA-seq
+  - Training (education)
+  - Workflow management systems
+  - Bioinformatics
+license: CC0

episodes/01-getting-started-with-nextflow.md

@@ -178,7 +178,7 @@ $ cp scripts/introduction/word_count.nf .
 ```groovy
 #!/usr/bin/env nextflow
 
-nextflow.enable.dsl=2
+
 
 /*
 ========================================================================================
@@ -243,13 +243,12 @@ process NUM_LINES {
 This is a Nextflow script, which contains the following:
 
 1. An optional interpreter directive ("Shebang") line, specifying the location of the Nextflow interpreter.
-2. `nextflow.enable.dsl=2` to enable DSL2 syntax.
-3. A multi-line Nextflow comment, written using C style block comments, there are more comments later in the file.
-4. A pipeline parameter `params.input` which is given a default value, of the relative path to the location of a compressed fastq file, as a string.
-5. A Nextflow channel `input_ch` used to read in data to the workflow.
-6. An unnamed `workflow` execution block, which is the default workflow to run.
-7. A call to the process `NUM_LINES`.
-8. An operation on the process output, using the channel operator `.view()`.
+2. A multi-line Nextflow comment, written using C style block comments, there are more comments later in the file.
+3. A pipeline parameter `params.input` which is given a default value, of the relative path to the location of a compressed fastq file, as a string.
+4. A Nextflow channel `input_ch` used to read in data to the workflow.
+5. An unnamed `workflow` execution block, which is the default workflow to run.
+6. A call to the process `NUM_LINES`.
+7. An operation on the process output, using the channel operator `.view()`.
 8. A Nextflow process block named `NUM_LINES`, which defines what the process does.
 9. An `input` definition block that assigns the `input` to the variable `read`, and declares that it should be interpreted as a file path.
 10. An `output` definition block that uses the Linux/Unix standard output stream `stdout` from the script block.

episodes/02-workflow_parameters.md

@@ -228,8 +228,8 @@ $ nextflow run wc-params.nf --sleep 1 --input 'data/yeast/reads/*.fq.gz'
 ## Parameter File
 
 If we have many parameters to pass to a script it is best to create a
-parameters file. Parameters are stored in JSON or YAML format. JSON and
-YAML are data serialization languages, that are a way of storing data
+parameters file. Parameters can be stored in JSON format. JSON is a
+data serialization language, that is a way of storing data
 objects and structures, such as the `params` object in a file.
 
 The `-params-file` option is used to pass the parameters file to the
@@ -306,5 +306,5 @@ f5ef7b7a01 executor \> local (1) [f3/4fa480] process \> NUM_LINES
 :::::::::::::::::::::::::::::::::::::::: keypoints
 - "Pipeline parameters are specified by prepending the prefix `params` to a variable name, separated by dot character."
 - "To specify a pipeline parameter on the command line for a Nextflow run use `--variable_name` syntax."
-- "You can add parameters to a JSON or YAML formatted file and pass them to the script using option `-params-file`."
+- "You can add parameters to a JSON formatted file and pass them to the script using option `-params-file`."
 ::::::::::::::::::::::::::::::::::::::::::::::::::

episodes/03-channels.md

@@ -49,16 +49,6 @@ Queue channels are a type of channel in which data is consumed (used up) to make
 1. As the outputs of a process.
 2. Explicitly using channel factory methods such as [Channel.of](https://www.nextflow.io/docs/latest/channel.html#of) or [Channel.fromPath](https://www.nextflow.io/docs/latest/channel.html#frompath).
 
-:::::::::::::::::::::::::::::::::::::::::  callout
-
-## DSL1
-
-In Nextflow DSL1 queue channels can only be used once in a workflow, either connecting workflow input to process input, or process output to input for another process.
-In DSL2 we can use a queue channel multiple times.
-
-
-::::::::::::::::::::::::::::::::::::::::::::::::::
-
 ### Value channels
 
 The second type of Nextflow channel is a `value` channel. A **value** channel is bound to a **single** value. A value channel can be used an unlimited number times since its content is not consumed. This is also useful for processes that need to reuse input from a channel, for example, a reference genome sequence file that is required by multiple steps within a process, or by more than one process.