Allow spaces in directory paths

[robsyme]

Currently, nf-core pipelines disallow spaces in directory paths, which unnecessarily limits usability. If users inherit datasets with spaces in the path (e.g., from external collaborators or legacy systems), they may be unable to run the pipeline without renaming files — a non-trivial operation, especially with object storage.

Nextflow stages inputs into isolated work directories, so spaces in source paths have no impact on tool execution. We continue to disallow spaces in filenames themselves to avoid downstream issues.

Allowing spaces in directory paths improves flexibility without compromising workflow robustness. Renaming paths is not always feasible (e.g., on object storage where renaming is non-atomic) and can break integrations with other systems.

[robsyme]

Example snippet (run nextflow console to check) that checks the regular expression matching:

// Define the regex as a plain string (with double backslashes!)
def regexString = "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$"

// Compile the regex string into a Pattern
def regex = Pattern.compile(regexString)

// Example list of paths
def paths = [
    "s3://path/to some/reads/RD-172.fastq.gz",   // valid
    "reads.fq.gz",                               // valid
    "reads.fastq.gz",                            // valid
    "path/reads.fastq.gz",                       // valid
    "path with space/reads.fastq.gz",            // valid
    "path/to some/reads.fq.gz",                  // valid
    "path/reads .fastq.gz",                      // invalid (space in filename)
    "path/reads.fastq",                          // invalid (missing .gz)
    "reads.fastq .gz"                            // invalid (space in filename)
]

// Validate each path
paths.each { path ->
    if (regex.matcher(path).matches()) {
        println "VALID:   $path"
    } else {
        println "INVALID: $path"
    }
}

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 76.47%. Comparing base (59f8aff) to head (01c091d).
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[maxulysse]

As seen in nf-core/rnafusion#659