nextflow.script.params.EachInParam.groovy Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of nextflow Show documentation
Show all versions of nextflow Show documentation
A DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner
/*
* 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.params
import groovy.transform.InheritConstructors
import groovy.transform.PackageScope
import groovy.util.logging.Slf4j
import groovyx.gpars.dataflow.DataflowReadChannel
import groovyx.gpars.dataflow.DataflowVariable
import groovyx.gpars.dataflow.expression.DataflowExpression
import nextflow.extension.CH
import nextflow.extension.ToListOp
import nextflow.script.TokenFileCall
import nextflow.script.TokenPathCall
/**
* Represents a process input *iterator* parameter
*
* @author Paolo Di Tommaso
*/
@InheritConstructors
@Slf4j
class EachInParam extends BaseInParam {
@Override String getTypeName() { 'each' }
private List inner = []
String getName() { '__$'+this.toString() }
Object clone() {
final copy = (EachInParam)super.clone()
copy.@inner = new ArrayList<>(inner.size())
for( BaseInParam p : inner ) {
copy.@inner.add((BaseInParam)p.clone())
}
return copy
}
EachInParam bind( def obj ) {
final nested = createNestedParam(obj)
nested.owner = this
this.bindObject = nested.bindObject
return this
}
protected BaseInParam createNestedParam(obj) {
if( obj instanceof TokenFileCall ) {
return new FileInParam(binding, inner, index)
.bind(obj.target)
}
if( obj instanceof TokenPathCall ) {
return new FileInParam(binding, inner, index)
.setPathQualifier(true)
.bind(obj.target)
}
return new ValueInParam(binding, inner, index)
.bind(obj)
}
InParam getInner() { inner[0] }
@Override
protected DataflowReadChannel inputValToChannel( value ) {
def variable = normalizeToVariable( value )
super.inputValToChannel(variable)
}
@PackageScope
DataflowReadChannel normalizeToVariable( value ) {
def result
if( value instanceof DataflowExpression ) {
result = value
}
else if( CH.isChannel(value) ) {
def read = CH.getReadChannel(value)
result = new ToListOp(read).apply()
}
else {
result = new DataflowVariable()
result.bind(value)
}
return result.chainWith { it instanceof Collection || it == null ? it : [it] }
}
}