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A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner

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/*
 * Copyright 2013-2024, Seqera Labs
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package nextflow.script

import groovy.transform.CompileStatic
import groovy.util.logging.Slf4j
import groovyx.gpars.dataflow.DataflowWriteChannel
import nextflow.exception.DuplicateChannelNameException
import nextflow.script.params.OutParam
import nextflow.script.params.OutputsList
import static nextflow.ast.NextflowDSLImpl.OUT_PREFIX
/**
 * Models the output of a process or a workflow component returning
 * more than one output channels
 *
 * @author Paolo Di Tommaso 
 */
@Slf4j
@CompileStatic
class ChannelOut implements List {

    // note: excludes 'reversed' to prevent issues caused by the introduction
    // of SequenceCollection by Java 21 when running on Java 20 or earlier
    // see: https://github.com/nextflow-io/nextflow/issues/5029
    @Delegate(excludes = ['reversed','addFirst','addLast','getFirst','getLast','removeFirst','removeLast'])
    private List target

    private Map channels

    ChannelOut() {
        this.target = Collections.unmodifiableList(Collections.emptyList())
        this.channels = Collections.emptyMap()
    }

    ChannelOut(List c) {
        this.target = Collections.unmodifiableList(c)
        this.channels = Collections.emptyMap()
    }

    ChannelOut(Map channels) {
        this.target = Collections.unmodifiableList(new ArrayList(channels.values()))
        this.channels = Collections.unmodifiableMap(new LinkedHashMap(channels))
    }

    ChannelOut(OutputsList outs) {
        channels = new HashMap<>(outs.size())
        final onlyWithName = new ArrayList(outs.size())
        for( OutParam param : outs ) {
            final ch = param.getOutChannel()
            final name = param.channelEmitName
            onlyWithName.add(ch)
            if(name) {
                if(channels.containsKey(name)) throw new DuplicateChannelNameException("Output channel name `$name` is used more than one time")
                channels.put(name, ch)
            }
        }
        target = Collections.unmodifiableList(onlyWithName)
    }

    Set getNames() { channels.keySet().findAll { !it.startsWith(OUT_PREFIX) }  }

    @Override
    def getProperty(String name) {
        if( this.channels.containsKey(name) ) {
            return channels.get(name)
        }
        else
            metaClass.getProperty(this,name)
    }

    /**
     * Helper method that convert the arguments array into a list expanding nested items of type
     * {@link ChannelOut} into the corresponding elements
     *
     * @param args
     *      The arguments array
     * @return
     *      A list of argument replacing item of type {@link ChannelOut} to the expanded elements
     */
    static List spread(Object[] args) {
        final result = new ArrayList(args.size()*2)
        for( int i=0; i