Improve lineage diagram

[bentsherman]

This PR makes the following improvements to the lineage diagram:

• Move render code to separate class
• Separate graph traversal from Mermaid rendering
• Distinguish task nodes from file nodes

I also removed the rendering of WorkflowRun nodes, because workflow runs are more like boundaries around nodes rather than nodes. We can try to add them later as subgraphs but for now I don't think it's important. We do need to make sure that the lineage can still be traced across multiple workflow runs.

Example lineage graph for the multiqc report produced by rnaseq-nf:

%%{
  init: {
    'theme': 'base',
    'themeVariables': {
      'primaryColor': '#B6ECE2',
      'primaryTextColor': '#160F26',
      'primaryBorderColor': '#065647',
      'lineColor': '#545555',
      'clusterBkg': '#BABCBD22',
      'clusterBorder': '#DDDEDE',
      'fontFamily': 'arial'
    }
  }
}%%
flowchart TB
    lid://9dd03aa13c2f2ecea7879aa1e50dba6e/summary/multiqc_report.html["lid://9dd03aa13c2f2ecea7879aa1e50dba6e/summary/multiqc_report.html"]
    lid://ef897bdf3c292346f76f82b24f7f0385/multiqc_report.html["lid://ef897bdf3c292346f76f82b24f7f0385/multiqc_report.html"]
    lid://ef897bdf3c292346f76f82b24f7f0385(["MULTIQC"])
    https://github.com/nextflow-io/rnaseq-nf/tree/73329b11f2d848c37e2c1ccdd923b327dae99d5f/multiqc["h‎ttps://github.com/nextflow-io/rnaseq-nf/tree/73329b11f2d848c37e2c1ccdd923b327dae99d5f/multiqc"]
    lid://82276016d8c7fbe8855dad0074bec31d/quant["lid://82276016d8c7fbe8855dad0074bec31d/quant"]
    lid://f2f2054d26f5a8457b49c47fa22f023f/fastqc["lid://f2f2054d26f5a8457b49c47fa22f023f/fastqc"]
    lid://82276016d8c7fbe8855dad0074bec31d(["RNASEQ:QUANT (gut)"])
    work/stage-21a4f7d6-11a8-4d56-b249-cc7a811eda6b/00/84ac54f3fe6eaad6bb24961e4f8d63/ggal_gut_1.fq["work/stage-21a4f7d6-11a8-4d56-b249-cc7a811eda6b/00/84ac54f3fe6eaad6bb24961e4f8d63/ggal_gut_1.fq"]
    work/stage-21a4f7d6-11a8-4d56-b249-cc7a811eda6b/43/c22c31954ad7b8f689adf7695c3e3a/ggal_gut_2.fq["work/stage-21a4f7d6-11a8-4d56-b249-cc7a811eda6b/43/c22c31954ad7b8f689adf7695c3e3a/ggal_gut_2.fq"]
    lid://f2f2054d26f5a8457b49c47fa22f023f(["RNASEQ:FASTQC (gut)"])
    work/stage-21a4f7d6-11a8-4d56-b249-cc7a811eda6b/00/84ac54f3fe6eaad6bb24961e4f8d63/ggal_gut_1.fq["work/stage-21a4f7d6-11a8-4d56-b249-cc7a811eda6b/00/84ac54f3fe6eaad6bb24961e4f8d63/ggal_gut_1.fq"]
    work/stage-21a4f7d6-11a8-4d56-b249-cc7a811eda6b/43/c22c31954ad7b8f689adf7695c3e3a/ggal_gut_2.fq["work/stage-21a4f7d6-11a8-4d56-b249-cc7a811eda6b/43/c22c31954ad7b8f689adf7695c3e3a/ggal_gut_2.fq"]
    lid://e93bfb52ddc455823173302ed4dff8d5/index["lid://e93bfb52ddc455823173302ed4dff8d5/index"]
    lid://e93bfb52ddc455823173302ed4dff8d5(["RNASEQ:INDEX (ggal_1_48850000_49020000)"])
    work/stage-21a4f7d6-11a8-4d56-b249-cc7a811eda6b/e7/181415b6783c942ef2d806c8023276/ggal_1_48850000_49020000.Ggal71.500bpflank.fa["work/stage-21a4f7d6-11a8-4d56-b249-cc7a811eda6b/e7/181415b6783c942ef2d806c8023276/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"]
    lid://ef897bdf3c292346f76f82b24f7f0385/multiqc_report.html --> lid://9dd03aa13c2f2ecea7879aa1e50dba6e/summary/multiqc_report.html
    lid://ef897bdf3c292346f76f82b24f7f0385 --> lid://ef897bdf3c292346f76f82b24f7f0385/multiqc_report.html
    lid://82276016d8c7fbe8855dad0074bec31d/quant --> lid://ef897bdf3c292346f76f82b24f7f0385
    lid://f2f2054d26f5a8457b49c47fa22f023f/fastqc --> lid://ef897bdf3c292346f76f82b24f7f0385
    https://github.com/nextflow-io/rnaseq-nf/tree/73329b11f2d848c37e2c1ccdd923b327dae99d5f/multiqc --> lid://ef897bdf3c292346f76f82b24f7f0385
    lid://82276016d8c7fbe8855dad0074bec31d --> lid://82276016d8c7fbe8855dad0074bec31d/quant
    lid://f2f2054d26f5a8457b49c47fa22f023f --> lid://f2f2054d26f5a8457b49c47fa22f023f/fastqc
    lid://e93bfb52ddc455823173302ed4dff8d5/index --> lid://82276016d8c7fbe8855dad0074bec31d
    work/stage-21a4f7d6-11a8-4d56-b249-cc7a811eda6b/00/84ac54f3fe6eaad6bb24961e4f8d63/ggal_gut_1.fq --> lid://82276016d8c7fbe8855dad0074bec31d
    work/stage-21a4f7d6-11a8-4d56-b249-cc7a811eda6b/43/c22c31954ad7b8f689adf7695c3e3a/ggal_gut_2.fq --> lid://82276016d8c7fbe8855dad0074bec31d
    work/stage-21a4f7d6-11a8-4d56-b249-cc7a811eda6b/00/84ac54f3fe6eaad6bb24961e4f8d63/ggal_gut_1.fq --> lid://f2f2054d26f5a8457b49c47fa22f023f
    work/stage-21a4f7d6-11a8-4d56-b249-cc7a811eda6b/43/c22c31954ad7b8f689adf7695c3e3a/ggal_gut_2.fq --> lid://f2f2054d26f5a8457b49c47fa22f023f
    lid://e93bfb52ddc455823173302ed4dff8d5 --> lid://e93bfb52ddc455823173302ed4dff8d5/index
    work/stage-21a4f7d6-11a8-4d56-b249-cc7a811eda6b/e7/181415b6783c942ef2d806c8023276/ggal_1_48850000_49020000.Ggal71.500bpflank.fa --> lid://e93bfb52ddc455823173302ed4dff8d5

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[bentsherman]

#5911 is needed to replace the work stage paths with the source URLs, I will try to get this resolved tomorrow

[jorgee]

I also removed the rendering of WorkflowRun nodes, because workflow runs are more like boundaries around nodes rather than nodes. We can try to add them later as subgraphs but for now I don't think it's important.

Not sure if we should remove this case. It was used to print the lineage when an output does not come from a task output. (such as the index file). In this case, the source of this output is the WorkflowRun. The render command was printing a dag with the data, the workflowRun and its params. With this PR it returns an error.

$ nextflow li render lid://ca2192600870bee8b13582afeae3808f/samples.json
ERROR: rendering lineage graph - Cannot render lineage for type WorkflowRun -- must be a FileOutput or TaskRun

before:

[bentsherman]

Good point, I have updated accordingly

I don't really like having non-file parameter values in the lineage graph as they are meaningless without their name (i.e. a workflow run having "2.0" as an input). But right now there is no way to distinguish between string and file inputs on the workflow run, so I'll leave it for now and we can refine when we have better typed inputs