error-ignore-then-fail.nf

#!/usr/bin/env nextflow
/*
 * Copyright 2013-2023, 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.
 */

workflow {
    input_channel = channel.of("SAMP1", "SAMP2", "SAMP3")
    foo(input_channel)
    bar(foo.out.sample_ids.collect())
}

process foo {
    input:
    val sample_id

    output:
    val sample_id, emit: sample_ids

    script:
    """
    if [[ $sample_id == "SAMP1" ]]; then
        exit 2
    fi
    ls -lah .*
    """
}

process bar {
    input:
    val ready

    output:
    stdout

    script:
    """
    ls -lah .*
    """

}