For creating the training environment there is no environment.yml file
Under the heading "Add Nextflow binary to your user’s PATH:"
the section "Check the correct installation running the following command:"
is accidentally repeated twice.
Getting started with nextflow
General comment: Pictures are rather small with small font.
Your first script section:
"Open the file wc.nf in the script directory with your favourite text editor."
could instead be
"Open the file "nf-training/scripts/introductions/wc.nf" with your favourite text editor.
Weird formatting of last comment in CODE section. (line breaking in "without")
Since the environment.yml file in introduction does not exist the reference to the nextflow
environment in nextflow config does not work as it is written now.
"We will learn how exactly nextflow using work directory to execute processes in the following sections."
could be:
"We will learn how exactly nextflow is using the work directory to execute processes in the following sections."
Nextflow scripting
This section would probably benefit from some more exercises with solutions. Otherwise fine.
Workflow parameterization
First section: "Objectives"
"Add a pipeline parameters to a Nextflow script."
Should be:
"Add pipeline parameters to a Nextflow script.
"Pipeline parameters"
"wild cards" should be replaced with "wildcards", right?
Channels
no comments on this section
Processes
no comments on this section
Processes Part 2
"Output values"
"...if we want to share a value input into one process as input to another process we would need..."
this wording is confusing to me (might have misunderstood this), shouldn't it read something like:
"...if we want to share a value output from one process as input to another process we would need..."
"Output files"
the example code is missing the "script:" line (should probably be there to be consistant with the rest of the examples)
Workflow
no comments on this section
Operators
The groovy keyword $it "(‘it’ is for ‘item’)" is first explained in this section although it is used several times in earlier examples.
Maybe introduce it like this first time it is encountered in the lectures.
"Grouping contents of a channel by a key."
Shouldn't the output of the first code example here be: "[wt, [wt_1.fq, wt_2.fq]]"
instead of "[wt, [wt_1.fq, wt_1.fq]]"?
Nextflow configuration
The section "Configuring Nextflow vs Configuring a Nextflow workflow"
is repeated twice by mistake.
"Inspecting the Nextflow configuration"
missing example output.
Simple RNA-Seq pipeline
Under objectives:
"Produce an execution report and generates run metrics from a pipeline run."
should read:
"Produce an execution report and generate run metrics from a pipeline run."
Had to change multiqc version in environment.yml (instructions point to old version that doesn't work on my mac) in order to get it to work
under "MultiQC report".
Modules
no comments on this section
Sub-workflows
Under heading "Workflow outputs":
"The output QUANT.out is assigned the name read_quant The the result of the above snippet can accessed using:"
should read:
The output QUANT.out is assigned the name read_quant. The result of the above snippet can accessed using:"
Under heading "Workflow composition":
"After which thet can then be invoked" should be "After which they can then be invoked"
Reporting
no comments on this section
Workflow caching and checkpointing
no comments on this section
Deploying nf-core pipelines
under heading "Sorting available nf-core pipelines":
"Archived pipelines are not returned by default. To include them, use the --show_archived flag."
should read:
"Archived pipelines are not returned by default. To include them, use the --show-archived flag."
Under heading "Running nf-core pipelines" and "Development Releases"
"For pipelines with a stable release this the default branch is..."
should be:
"For pipelines with a stable release the default branch is..."
under heading "Config files" point 2 in the list:
"There two test profile,..." should read "There are two test profiles,..."
Notes for Mahesh with comments on Nextflow course material (https://carpentries-incubator.github.io/workflows-nextflow/):
SETUP section:
For creating the training environment there is no environment.yml file
Under the heading "Add Nextflow binary to your user’s PATH:" the section "Check the correct installation running the following command:" is accidentally repeated twice.
Getting started with nextflow
General comment: Pictures are rather small with small font.
Your first script section: "Open the file wc.nf in the script directory with your favourite text editor." could instead be "Open the file "nf-training/scripts/introductions/wc.nf" with your favourite text editor.
Weird formatting of last comment in CODE section. (line breaking in "without")
Since the environment.yml file in introduction does not exist the reference to the nextflow environment in nextflow config does not work as it is written now.
"We will learn how exactly nextflow using work directory to execute processes in the following sections." could be: "We will learn how exactly nextflow is using the work directory to execute processes in the following sections."
Nextflow scripting
This section would probably benefit from some more exercises with solutions. Otherwise fine.
Workflow parameterization
First section: "Objectives" "Add a pipeline parameters to a Nextflow script." Should be: "Add pipeline parameters to a Nextflow script.
"Pipeline parameters" "wild cards" should be replaced with "wildcards", right?
Channels
no comments on this section
Processes
no comments on this section
Processes Part 2
Workflow
no comments on this section
Operators
The groovy keyword $it "(‘it’ is for ‘item’)" is first explained in this section although it is used several times in earlier examples. Maybe introduce it like this first time it is encountered in the lectures.
"Grouping contents of a channel by a key." Shouldn't the output of the first code example here be: "[wt, [wt_1.fq, wt_2.fq]]" instead of "[wt, [wt_1.fq, wt_1.fq]]"?
Nextflow configuration
The section "Configuring Nextflow vs Configuring a Nextflow workflow" is repeated twice by mistake.
"Inspecting the Nextflow configuration" missing example output.
Simple RNA-Seq pipeline
Under objectives: "Produce an execution report and generates run metrics from a pipeline run." should read: "Produce an execution report and generate run metrics from a pipeline run."
Had to change multiqc version in environment.yml (instructions point to old version that doesn't work on my mac) in order to get it to work under "MultiQC report".
Modules
no comments on this section
Sub-workflows
Under heading "Workflow outputs": "The output QUANT.out is assigned the name read_quant The the result of the above snippet can accessed using:"
should read: The output QUANT.out is assigned the name read_quant. The result of the above snippet can accessed using:"
Under heading "Workflow composition":
"After which thet can then be invoked" should be "After which they can then be invoked"
Reporting
no comments on this section
Workflow caching and checkpointing
no comments on this section
Deploying nf-core pipelines
under heading "Sorting available nf-core pipelines":
"Archived pipelines are not returned by default. To include them, use the --show_archived flag." should read: "Archived pipelines are not returned by default. To include them, use the --show-archived flag."
Under heading "Running nf-core pipelines" and "Development Releases" "For pipelines with a stable release this the default branch is..." should be: "For pipelines with a stable release the default branch is..."
under heading "Config files" point 2 in the list:
"There two test profile,..." should read "There are two test profiles,..."