Skip to content

--igenomes_base could not validate file format #605

Description

@Blondeau-Bidet

Description of the bug

Hello,

When I run my job, I get the following error message: * --igenomes_base (s3://ngi-igenomes/igenomes/): could not validate file format of 's3://ngi-igenomes/igenomes/': Missing plugin 'nf-amazon' required to read file: s3://ngi-igenomes/igenomes/.
It seems this is a known issue: nextflow-io/nf-schema#204. But in practical terms, how can I work around the problem? My skills are fairly limited beyond the basic pipeline settings. Do you have any idea how long it might take to resolve this issue ?

Thank you

Command used and terminal output

nextflow run main.nf -profile singularity -c ${CONFIG} -ansi-log false \
--outdir /Results \
--input samplesheet_test.csv \
--fasta hap1.sm.fasta \
--em_seq \
--cytosine_report \
--multiQC_title EMseq_test

Relevant files

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 'subworkflows/nf-core/utils_nfschema_plugin/main.nf' at line: 68 or see '.nextflow.log' file for more details

System information

N E X T F L O W ~ version 25.04.4
Launching main.nf [nasty_borg] DSL2 - revision: c774a185d2
nf-core-methylseq_4.2.0
Container engine Singularity
Hardware HPC
Executor PBS

Metadata

Metadata

Assignees

No one assigned

    Labels

    bugSomething isn't working

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions