ampa.nf

#!/usr/bin/env nextflow 
/*
 * Copyright 2020-2022, Seqera Labs
 * Copyright 2013-2019, Centre for Genomic Regulation (CRG)
 *
 * 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.
 */
nextflow.enable.dsl=1

params.in = "$baseDir/data/sample.fa"

/*
 * Splits the input file in chunks containing a single sequences,
 * and send each of it over the 'seq' channel
 */
seq = Channel.fromPath(params.in).splitFasta()

/*
 * For each sequence that is sent over the 'seq' channel
 * the below task is executed
 */
process ampaTask {

    input:
    file seq

    output:
    file result

    // The BASH script to be executed - for each - sequence
    """
    AMPA.pl -in=${seq} -noplot -rf=result -df=data
    """

}

/*
 * print out each 'result' produced by the above step
 */
result.subscribe { println it.text }