nf-core / nf-core/methylseq

--igenomes_base could not validate file format

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bug
Dominant language
Nextflow
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198
Forks
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Avg merge
6d 17h
Merged PRs (30d)
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Description

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: https://github.com/nextflow-io/nf-schema/issues/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

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with subworkflows/nf-core/utils_nfschema_plugin/main.nf at line 68 and the .nextflow.log referenced in the report. Reproduce the --igenomes_base validation failure with the supplied command and inspect how the pipeline handles the missing plugin or unreachable S3 path. Done means the reported input is validated successfully or the issue documents a confirmed workaround.

Written by the indexing model from the issue text.

Assessment

Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Needs clarification
Newbie friendliness
35/100

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