offline mode not working in 3.22.2 unless --igenomes_base is set to a dummy path

[JKing2000]

Description of the bug

We have set up rnaseq version 3.22.2 the same way as version 3.21.0 on nci-gadi but offline mode no longer works unless --igenomes_base is set to a dummy path. This seems to not be an issue in older version where the default values of --igenomes_base is ignored when set to offline mode.

Command used and terminal output

export NXF_OFFLINE="true"
cd /path/to/workingdir

nextflow -c ${WF_HOME}/config/nci_gadi.config run ${WF_HOME}/rnaseq \
-profile singularity \
--input samplesheet.csv \
--fasta reference_assembly.fasta.gz \
--gtf complete.genomic.gtf \
--outdir /path/to/outputdir


ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --igenomes_base (s3://ngi-igenomes/igenomes/): could not validate file format of 's3://ngi-igenomes/igenomes/': Unable to execute HTTP request: Network is unreachable

 -- Check script '/g/data/cy20/workflows/rnaseq/3.22.2/rnaseq/subworkflows/nf-core/utils_nfschema_plugin/main.nf' at line: 68 or see '.nextflow.log' file for more details

Relevant files

.nextflow.log

System information

Nextflow version: 25.04.6
Hardware: HPC, NCI-gadi
Executor: pbspro
Container engine: singularity
OS: Rocky Linux 8.10 (Green Obsidian)
Version of nf-core/rnaseq: 3.22.2

[kisarur]

This seems to be due to rnaseq v3.22.2 using the updated nf-schema@2.5.1 plugin (compared to nf-schema@2.4.2 in rnaseq v3.21.0). Starting from nf-schema@2.5.0, the plugin seems to validate cloud storage paths instead of skipping them (see "Changes" here). As a result, the plugin now tries to validate igenomes_base which by default points to "s3://ngi-igenomes/igenomes/" by making external network calls.

If you need to run the Nextflow head job on an NCI-Gadi node with no external network access, an alternative workaround would be to disable validation for igenomes_base by adding the following to your config:

validation.ignoreParams = ["igenomes_base"]

[pinin4fjords]

Thanks for reporting this @JKing2000, and thanks @kisarur for the analysis and workaround.

I've opened nextflow-io/nf-schema#204 to track the upstream fix, and #1696 adds the workaround to the pipeline config so future releases won't be affected.

In the meantime, you can work around this by adding the following to your Nextflow config:

validation.ignoreParams = ["igenomes_base"]