What do you need to know about processes in nextflow?

What do you need to know about processes in nextflow?

In Nextflow a process is the basic processing primitive to execute a user script. The process definition starts with keyword the process, followed by process name and finally the process body delimited by curly brackets. The process body must contain a string which represents the command or, more generally, a script that is executed by it.

How does the FILTER operator work in nextflow?

The filter operator allows you to get only the items emitted by a channel that satisfy a condition and discarding all the others. The filtering condition can be specified by using either a regular expression , a literal value, a type qualifier (i.e. a Java class) or any boolean predicate.

What kind of script is used in nextflow?

The process script is interpreted by Nextflow as a Bash script by default, but you are not limited to it. You can use your favourite scripting language (e.g. Perl, Python, Ruby, R, etc), or even mix them in the same pipeline.

What does the shell block do in nextflow?

The shell block is a string statement that defines the shell command executed by the process to carry out its task. It is an alternative to the Script definition with an important difference, it uses the exclamation mark ! character as the variable placeholder for Nextflow variables in place of the usual dollar character.

How to create execution trace file in nextflow?

Nextflow creates an execution tracing file that contains some useful information about each process executed in your pipeline script, including: submission time, start time, completion time, cpu and memory used. In order to create the execution trace file add the -with-trace command line option when launching the pipeline execution.

Which is the second input in nextflow containerization?

Also note as the second input is declared as a set composed by two elements: the pair_id and the reads in order to match the structure of the items emitted by the read_pairs_ch channel. You will see the execution of a quantication process. Execute it again adding the -resume option as shown below:

How to parallelize the execution of a pipeline in nextflow?

Nextflow parallelizes the execution of your pipeline simply by providing multiple input data to your script. Add a tag directive to the quantification process to provide a more readable execution log . Add a publishDir directive to the quantification process to store the process results into a directory of your choice.

Which is a property of a channel in nextflow?

Nextflow is based on the Dataflow programming model in which processes communicate through channels. A channel has two major properties: Sending a message is an asynchronous operation which completes immediately, without having to wait for the receiving process.

What kind of programming language does nextflow use?

Groovy is a powerful programming language for the Java virtual machine. The Nextflow syntax has been specialized to ease the writing of computational pipelines in a declarative manner. Nextflow can execute any piece of Groovy code or use any library for the JVM platform.

How does the fromfilepairs method work in nextflow?

The fromFilePairs method creates a channel emitting the file pairs matching a glob pattern provided by the user. The matching files are emitted as tuples in which the first element is the grouping key of the matching pair and the second element is the list of files (sorted in lexicographical order).

Where do I find my template in nextflow?

A template is simply a shell script file that Nextflow is able to execute by using the template function as shown below: Nextflow looks for the my_script.sh template file in the directory templates that must exist in the same folder where the Nextflow script file is located (any other location can be provided by using an absolute template path).

How to move nextflow file to new directory?

Optionally, move the nextflow file to a directory accessible by your $PATH variable (this is only required to avoid remembering and typing the full path to nextflow each time you need to run it). Set export CAPSULE_LOG=none to make the dependency installation logs less verbose.