Allow collection-type params to be loaded from files

[bentsherman]

This PR adds the ability to declare a param as a collection type:

params {
  input: List<Map>
}

workflow {
  println params.input*.id.join(',')
}

And supply a CSV, JSON, or YAML file at runtime:

$ cat input.json
[
  { "id": "1", "fastq": "data/1.fastq" },
  { "id": "2", "fastq": "data/2.fastq" },
  { "id": "3", "fastq": "data/3.fastq" }
]

$ nextflow run main.nf --input input.json
1,2,3

Nextflow interprets the string as a file path and attempts to load the file contents based on the file extension. A runtime error is reported if the file contents are not compatible with the declared type.

Future work will extend the type validation with record types.

(spun off from #6574)

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[christopher-hakkaart]

Docs look good. No comments.

[jorgee]

I have been testing with other standard library objects, and it is working with Set and List, but not with Bag, IterableandMap`.

• It is not possible to cast the ArrayList object returned by the slurpers to a Bag. I think it should be supported as in the documentation clearly says that Bag is a Collection.
• Iterable is a superinterface of Collection
• Map is not a Collection, but there is a direct mapping of YAML and JSON files with Maps.

Not sure if it was the goal of the PR to support all the types, but I see it is possible with very little changes. I have created #6676 to support all these types.

[bentsherman]

Thanks Jorge. I intentionally did not support Iterable and Map because I'm not sure about those cases yet. But I did intend to support Bag so thank you for catching that

[jorgee]

@pditommaso the bump of Netty version is producing failures in azure tests

java.lang.IllegalArgumentException: The URI contain illegal characters: /my-data?restype=container&comp=list&prefix=work/4a/332d3d24a0334ab4b84d8992095d35&marker=2%21120%21MDAwMDQ0IXdvcmsvNGEvMzMyZDNkMjRhMDMzNGFiNGI4NGQ4OTkyMDk1ZDM1L2YxLmZhITAwMDAyOCE5OTk5LTEyLTMxVDIzOjU5OjU5Ljk5OTk5OTlaIQ--&maxresults=10
	at io.netty.handler.codec.http.HttpUtil.validateRequestLineTokens(HttpUtil.java:90)
	at io.netty.handler.codec.http.DefaultHttpRequest.<init>(DefaultHttpRequest.java:95)
	at io.netty.handler.codec.http.DefaultFullHttpRequest.<init>(DefaultFullHttpRequest.java:103)
	at io.netty.handler.codec.http.DefaultFullHttpRequest.<init>(DefaultFullHttpRequest.java:95)
	at io.netty.handler.codec.http.DefaultFullHttpRequest.<init>(DefaultFullHttpRequest.java:87)
	at io.netty.handler.codec.http.DefaultFullHttpRequest.<init>(DefaultFullHttpRequest.java:50)
	at reactor.netty.http.client.HttpClientOperations.newFullBodyMessage(HttpClientOperations.java:884)
	at reactor.netty.http.client.HttpClientOperations.lambda$send$2(HttpClientOperations.java:913)
	at reactor.netty.FutureMono$DeferredFutureMono.subscribe(FutureMono.java:100)
	at reactor.core.publisher.MonoDefer.subscribe(MonoDefer.java:53)
	at reactor.netty.http.client.HttpClientConnect$HttpIOHandlerObserver.onStateChange(HttpClientConnect.java:459)
	at reactor.netty.ReactorNetty$CompositeConnectionObserver.onStateChange(ReactorNetty.java:722)
	at reactor.netty.resources.DefaultPooledConnectionProvider$DisposableAcquire.run(DefaultPooledConnectionProvider.java:294)
	at io.netty.util.concurrent.AbstractEventExecutor.runTask(AbstractEventExecutor.java:173)
	at io.netty.util.concurrent.AbstractEventExecutor.safeExecute(AbstractEventExecutor.java:166)
	at io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:472)
	at io.netty.channel.epoll.EpollEventLoop.run(EpollEventLoop.java:405)
	at io.netty.util.concurrent.SingleThreadEventExecutor$4.run(SingleThreadEventExecutor.java:998)
	at io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74)
	at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30)
	at java.base/java.lang.Thread.run(Thread.java:1447)
Dec-19 14:18:51.285 [TaskFinalizer-1] ERROR c.a.c.h.netty.NettyAsyncHttpClient - The URI contain illegal characters: /my-data?restype=container&comp=list&prefix=work/4a/332d3d24a0334ab4b84d8992095d35&marker=2%21120%21MDAwMDQ0IXdvcmsvNGEvMzMyZDNkMjRhMDMzNGFiNGI4NGQ4OTkyMDk1ZDM1L2YxLmZhITAwMDAyOCE5OTk5LTEyLTMxVDIzOjU5OjU5Ljk5OTk5OTlaIQ--&maxresults=10
Dec-19 14:18:51.285 [TaskFinalizer-1] ERROR c.a.s.c.policy.RequestRetryPolicy - The URI contain illegal characters: /my-data?restype=container&comp=list&prefix=work/4a/332d3d24a0334ab4b84d8992095d35&marker=2%21120%21MDAwMDQ0IXdvcmsvNGEvMzMyZDNkMjRhMDMzNGFiNGI4NGQ4OTkyMDk1ZDM1L2YxLmZhITAwMDAyOCE5OTk5LTEyLTMxVDIzOjU5OjU5Ljk5OTk5OTlaIQ--&maxresults=10
Dec-19 14:18:51.285 [TaskFinalizer-1] ERROR c.a.s.c.i.StorageImplUtils - null
Dec-19 14:18:51.442 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=foo; work-dir=az://my-data/work/4a/332d3d24a0334ab4b84d8992095d35
  error [java.lang.RuntimeException]: java.lang.RuntimeException
Dec-19 14:18:51.450 [TaskFinalizer-1] ERROR nextflow.processor.TaskProcessor - Error executing process > 'foo'

Caused by:
  java.lang.RuntimeException


java.lang.RuntimeException: null
	at com.azure.storage.common.implementation.StorageImplUtils.sendRequest(StorageImplUtils.java:511)
	at com.azure.storage.blob.BlobContainerClient.lambda$listBlobs$7(BlobContainerClient.java:1050)
	at com.azure.core.http.rest.PagedIterable.lambda$new$5(PagedIterable.java:194)
	at com.azure.core.util.paging.ContinuablePagedByIteratorBase.requestPage(ContinuablePagedByIteratorBase.java:104)
	at com.azure.core.util.paging.ContinuablePagedByIteratorBase.hasNext(ContinuablePagedByIteratorBase.java:65)
	at nextflow.cloud.azure.nio.AzFileSystem$_guessPath_lambda10.doCall(AzFileSystem.groovy:395)
	at dev.failsafe.Functions.lambda$toCtxSupplier$11(Functions.java:236)
	at dev.failsafe.Functions.lambda$get$0(Functions.java:46)
	at dev.failsafe.internal.RetryPolicyExecutor.lambda$apply$0(RetryPolicyExecutor.java:75)
	at dev.failsafe.SyncExecutionImpl.executeSync(SyncExecutionImpl.java:176)
	at dev.failsafe.FailsafeExecutor.call(FailsafeExecutor.java:437)
	at dev.failsafe.FailsafeExecutor.get(FailsafeExecutor.java:115)
	at nextflow.cloud.azure.nio.AzFileSystem.apply(AzFileSystem.groovy:564)