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Output DSL not creating parent directory. #5465

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Joon-Klaps opened this issue Nov 4, 2024 · 0 comments · May be fixed by #5502
Open

Output DSL not creating parent directory. #5465

Joon-Klaps opened this issue Nov 4, 2024 · 0 comments · May be fixed by #5502
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@Joon-Klaps
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Bug report

Expected behavior and actual behavior

Using output dsl as specified in docs for creating a samplesheet of a channel. Throws an ERROR ~ No such file or directory, when I would expect it to just create the file with it's correct parent dirs.

Steps to reproduce the problem

#!/usr/bin/env nextflow

nextflow.preview.output = true
workflow {
    main:
    ch_fastq = Channel.of(
        [ [id: 1, name: 'sample 1'], '1a.fastq', '1b.fastq' ],
        [ [id: 2, name: 'sample 2'], '2a.fastq', '2b.fastq' ],
        [ [id: 3, name: 'sample 3'], '3a.fastq', '3b.fastq' ]
    )

    publish:
    ch_fastq >> 'fastq'

}

output {
    'fastq' {
        index {
            path 'index.csv'
        }
    }
}
 NXF_VER=24.10.0 nextflow run . -output-dir testing

dummy - repo

Program output


 N E X T F L O W   ~  version 24.10.0

Launching `./main.nf` [ecstatic_shirley] DSL2 - revision: f3a7b194c5

WARN: WORKFLOW OUTPUT DSL IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
ERROR ~ No such file or directory: /workspace/Nextflow_sandbox/testing/fastq/index.csv

 -- Check '.nextflow.log' file for details

nextflow.log

Environment

  • Nextflow version: 24.10.0
  • Java version: 17.0.11-internal 2024-04-16
  • Operating system: Linux
  • Bash version: 5.1.16(1)-release
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