Reporting in Cloudgene¶

Cloudgene supports reporting by parsing the standard output (stdout) of each process it runs. This allows users to generate detailed logs and reports using specific output commands. The functionality is similar to GitHub Actions, utilizing annotations and groups to organize and present information effectively.

Example¶

main.nf cloudgene.yaml Output

params.n = 5 // Default number of quotes to extract

process extractRandomQuote {
    input:
    path quotesFile
    val index

    script:
    """
    QUOTE=`shuf ${quotesFile} | head -n 1`
    echo "::message::\${QUOTE}"
    """
}

workflow {
    extractRandomQuote(
        file("${projectDir}/quotes.txt"),
        Channel.of(1..params.n)
    )
}

id: hello-cg
name: Hello CG
version: 1.0
workflow:
steps:
- name: Get quotes
  script: main.nf

Output Commands¶

Cloudgene recognizes a series of specific commands in the stdout that help classify and structure log messages. Below is a list of supported commands and their usage:

Error Messages¶

To log an error message:

echo "::error::This is an error message"

General Messages¶

To log a general message:

echo "::message::This is a message"

Notices¶

To log a notice message:

echo "::notice::This is a notice message"

Warnings¶

To log a warning message:

echo "::warning::This is a warning message"

Debug Messages¶

To log a debug message:

echo "::debug::This is a debug message"

Grouping Messages¶

Cloudgene allows grouping of related log messages to enhance readability. Groups can have a specified type (e.g., error, warning) to provide additional context. Use the following commands to start and end a group:

Start a Group¶

To start a group:

echo "::group type=error::"

This will group subsequent log messages until the group is closed.

End a Group¶

To end a group:

echo "::endgroup::"

Example Group¶

echo "::group type=error::"
echo "This is a list:"
echo "- Line 1"
echo "- Line 2"
echo "::endgroup::"

In this example, the messages "This is a list:", "- Line 1", and "- Line 2" will be grouped together under an error type.

Counters¶

Cloudgene supports setting and submitting counters, which can be useful for tracking various metrics during the execution of a process.

Set a Counter¶

To set a counter with a specific name and value:

echo "::set-counter name=genomes::55"

Submit a Counter¶

To submit a counter, which can then be used for further processing or reporting:

echo "::submit-counter name=genomes::"