Azure path incorrectly determined to be directory by trailing slash #6427
Description
Bug report
If using nf-schema, Nextflow will determine an Azure path to be a directory if it's missing a trailing slash:
ERROR ~ Validation of pipeline parameters failed! -- Check '.nextflow.log' file for details The following invalid input values have been detected: * --outdir (az://pipeline/output): 'az://pipeline/output' is not a directory, but a file -- Check script '/home/username/.nextflow/assets/nf-core/rnaseq/subworkflows/nf-core/utils_nfschema_plugin/main.nf' at line: 39 or see '.nextflow.log' file for more details Expected behavior and actual behavior
nf-schema checks Nextflow.file.directory for whether a file is a directory, but for Azure this is inaccurate because it's just checking for the trailing slash:
For most situations, this is fine but when using nf-schema this becomes an issue because it halts the pipeline.
Instead, we should be able to have a more robust way of checking if the file is a directory on Azure, it's probably possible using the SDKs.
I will add a bypass for nf-schema.
Steps to reproduce the problem
main.nf:
// Print the parameters for inspection log.info """ Parameters: s3_file: ${params.s3_file ?: 'not set'} gs_file: ${params.gs_file ?: 'not set'} az_file: ${params.az_file ?: 'not set'} """ workflow { println "Cloud path validation example completed successfully!" } nextflow_schema.json:
{ "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/nf-schema/master/examples/cloudpath/nextflow_schema.json", "title": "Cloud path validation example", "description": "Example demonstrating cloud path validation", "type": "object", "properties": { "s3_file": { "type": "string", "format": "file-path", "description": "An S3 file path" }, "gs_file": { "type": "string", "format": "file-path", "description": "A Google Cloud Storage file path" }, "az_file": { "type": "string", "format": "file-path", "description": "An Azure Blob Storage file path" } } } Program output
(Copy and paste the output produced by the failing execution. Please highlight it as a code block. Whenever possible upload the .nextflow.log file.)
Environment
- Nextflow version: 25.04.7 build 5955
- nf-schema version: 2.5.1
- Java version: openjdk version "17.0.3" 2022-04-19
- Operating system: macOS
- Bash version: zsh
Additional context
Slack thread: https://nextflow.slack.com/archives/C02TPRRLCF4/p1758724547528979?thread_ts=1727918072.021049&cid=C02TPRRLCF4
nf-schema issue: nextflow-io/nf-schema#16