Print workflow outputs on run completion

[bentsherman]

Spun off from #6574

This PR updates OutputDsl to print the workflow outputs at the end of a run.

By default it prints a human-readable summary. You can set -output-format json to output JSON instead.

It has no effect when there is no output block

When combined with -q, it is useful for printing a comprehensive pipeline output that can be passed to downstream operations

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[pditommaso]

This could be useful in several scenarios. Could not make sense to print it by default in human readable manner and use an output format flag to switch to json, similarly to module run?

[bentsherman]

Yes I would be happy to always print something for the output.

The -o option is already used by the run command to specify the output directory, so we would probably call it -output-format

[bentsherman]

@jorgee if I add an -output-format option to the run command then you could reuse it in module run to control the output format like we were saying

[jorgee]

@jorgee if I add an -output-format option to the run command then you could reuse it in module run to control the output format like we were saying

This will fit perfect for module run.

[bentsherman]

Updated to print human-readable output by default.

This is what it looks like for the output-dsl.nf test:

[bentsherman]

Refining the output:

Outputs:

  /home/bent/projects/nextflow-io/nextflow/tests/checks/output-dsl.nf/results

  samples:
    - {id: sample9, fastqc: log/sample9.fastqc.log, bam: null, bai: null, quant: quant/sample9}
    - {id: sample4, fastqc: log/sample4.fastqc.log, bam: null, bai: null, quant: quant/sample4}
    - {id: sample5, fastqc: log/sample5.fastqc.log, bam: null, bai: null, quant: quant/sample5}
    - {id: sample15, fastqc: log/sample15.fastqc.log, bam: null, bai: null, quant: quant/sample15}
    - {id: sample8, fastqc: log/sample8.fastqc.log, bam: null, bai: null, quant: quant/sample8}
    - {id: sample11, fastqc: log/sample11.fastqc.log, bam: null, bai: null, quant: quant/sample11}
    - {id: sample1, fastqc: log/sample1.fastqc.log, bam: null, bai: null, quant: quant/sample1}
    - {id: sample14, fastqc: log/sample14.fastqc.log, bam: null, bai: null, quant: quant/sample14}
    - {id: sample6, fastqc: log/sample6.fastqc.log, bam: null, bai: null, quant: quant/sample6}
    - {id: sample3, fastqc: log/sample3.fastqc.log, bam: null, bai: null, quant: quant/sample3}
    - ... (90 more items)

  summary:
    - summary_report.html
    - summary_data/data.json
    - summary_data/fastqc.txt

[pditommaso]

it looks nice! is it aligned with modules output? or the other way around?

[bentsherman]

It is now 😄

$ nextflow -q module run test/my-test-module --meta.id 42 --id 42 --text input.txt --reads sample.fastq 
Outputs:

  /home/bent/projects/sketches/module-system-example/results

  txt:
    - {id: '42'}
    - out-42.txt

  id: '42'

$ nextflow -q module run test/my-test-module --meta.id 42 --id 42 --text input.txt --reads sample.fastq -output-format json
{
    "txt": [
        {
            "id": "42"
        },
        "/home/bent/projects/sketches/module-system-example/results/out-42.txt"
    ],
    "id": "42"
}

[pditommaso]

Cool, i'll play hard with modules this w-e