Dump pipeline parameters into a json file #2425
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Should we also add a |
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what's the difference to |
Codecov Report
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## dev #2425 +/- ##
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Coverage 71.07% 71.07%
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Files 87 87
Lines 9431 9431
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Hits 6703 6703
Misses 2728 2728
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Here the idea is to keep all the parameters as they have been used for a given execution in a |
| def jsonStr = "" | ||
| jsonStr = JsonOutput.toJson(params) |
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| def jsonStr = "" | |
| jsonStr = JsonOutput.toJson(params) | |
| def jsonStr = JsonOutput.toJson(params) |
| output_d.mkdirs() | ||
| } | ||
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| def output_pf = new File(output_d, "params.json") |
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I suspect that this will crash if the file already exists (eg. When resuming a pipeline). We should probably try to avoid this by checking if the file already exists, and/or incorporating a timestamp into the filename.
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I tested it and it did not crashed but yes, probably better to be in the safe lane, now is updated
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I think I have addressed your comments @mirpedrol and @ewels. Do you think we have to create a parameter to control for it? |
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Looks OK to me to always generate this file, I wouldn't add a parameter. |
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👀 👀 👀 so I know when to try adding to MultiQC ;) |
@jfy133 its after MultiQC runs, so won't be possible as it stands. It's also all parameters, so very verbose. |
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Sure, but presumably one could run the function before on complete, right? For the verboseness I was expecting that, as a second step I was actually wondering if it would be possible to make a collapsible section in the MultiQC report 😬 |
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Sure, but presumably one could run the function before on complete, right? For the verboseness I was expecting that, as a second step I was actually wondering if it would be possible to make a collapsible section in the MultiQC report 😬 |
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@jfy133 yes I also thought about it, probably for the MultiQC report it will be an option to do something similar to what |
public static void dump_parameters(workflow, params) {maybe a dumb question but why is |
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also I am wondering if this would still work if the |
Add to the template the snippet proposed on this comment to dump the pipeline parameters into a json file that can be use to re-run the pipeline with the same parameters using the
-params-fileNextflow option.Closes #747
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