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Merged
bentsherman merged 1 commit into from
Oct 10, 2023
Merged

Add task dag format #12

bentsherman merged 1 commit into from
Oct 10, 2023

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@bentsherman
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@bentsherman bentsherman commented Sep 28, 2023

Render the task graph as an HTML document, originally developed in nextflow-io/nextflow#3802

@samuell I was originally going to add your visualizer script, but then I realized we could just render the DAG directly in the plugin! I already wrote the code in a Nextflow PR but i think it fits better here. The task DAG is a sort of provenance report after all... anyway, want to give it a try and let me know if it can be improved at all?

Here is an example diagram for an rnaseq-nf run:

<html>
<head>
<meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
</head>
<body>
<pre class="mermaid" style="text-align: center;">
flowchart TD
    subgraph " "
    in0["ggal_gut_1.fq"]
    click in0 href "https://github.com/nextflow-io/rnaseq-nf/tree/d910312506c6539365ed70aacda5068dea9152dd/data/ggal/ggal_gut_1.fq" _blank
    in1["ggal_gut_2.fq"]
    click in1 href "https://github.com/nextflow-io/rnaseq-nf/tree/d910312506c6539365ed70aacda5068dea9152dd/data/ggal/ggal_gut_2.fq" _blank
    in2["ggal_1_48850000_49020000.Ggal71.500bpflank.fa"]
    click in2 href "https://github.com/nextflow-io/rnaseq-nf/tree/d910312506c6539365ed70aacda5068dea9152dd/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa" _blank
    in3["multiqc"]
    click in3 href "https://github.com/nextflow-io/rnaseq-nf/tree/d910312506c6539365ed70aacda5068dea9152dd/multiqc" _blank
    end
    subgraph RNASEQ
    t0(["FASTQC (FASTQC on ggal_gut)"])
    t1(["INDEX (ggal_1_48850000_49020000)"])
    t2(["QUANT (ggal_gut)"])
    end
    t3(["MULTIQC"])
    in0 --> t0
    in1 --> t0
    in2 --> t1
    t1 -->|index| t2
    in0 --> t2
    in1 --> t2
    t2 -->|ggal_gut| t3
    t0 -->|fastqc_ggal_gut_logs| t3
    in3 --> t3
    t3 --> out0
    subgraph " "
    out0[multiqc_report.html]
    end
</pre>
<script type="module">
  import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@10/dist/mermaid.esm.min.mjs';
  mermaid.initialize({ startOnLoad: true });
</script>
</body>
</html>

@bentsherman
Add task dag format
822f8fe 
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
@samuell
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samuell commented Sep 30, 2023

@bentsherman Cool, hope to have a look in the beginning of next week!

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bentsherman commented Oct 10, 2023

I'm gonna move this forward, but feel free to share any feedback here at your convenience. Not an urgent thing by any means

@bentsherman bentsherman merged commit a0f0dd4 into master Oct 10, 2023
@bentsherman bentsherman deleted the task-dag branch October 10, 2023 14:09
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3 participants

@bentsherman @samuell