nf-core / nf-core/radseq

Test data is not available

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bug
Dominant language
Nextflow
Stars
7
Forks
7
PR merge metrics
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Description

Description of the bug

I tried running a pipeline level test for nf-core/radseq on our HPC, and I got the following error:

ERROR ~ No such file or directory: https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/samplesheet/samplesheet_test_lpolyphemus_ddrad_sbfi_mluci.csv

I believe I found the correct samplesheet here.

When I ran the pipeline with this samplesheet and against the hsc_Chr26.fasta.gz reference, I got the following error:

ERROR ~ A process input channel evaluates to null -- Invalid declaration `val sequence_type`
Command used and terminal output
nextflow run nf-core/radseq -r dev -profile test,singularity --outdir $OUTDIR -w $WORKDIR -c $CONFIG
Relevant files

No response

System information
  • Nextflow version: 25.04.4
  • Hardware: HPC
  • Executor: slurm
  • Container engine: Singularity
  • OS: Ubuntu Linux
  • Version of nf-core/radseq: dev

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 by running the reported Nextflow command with the test profile and comparing the referenced radseq samplesheet and hsc_Chr26.fasta.gz URLs with the available test-datasets files. Trace the test inputs that produce the null sequence_type value; done means the test pipeline can access its data and proceeds without either reported error.

Written by the indexing model from the issue text.

Assessment

Domain
bioinformatics
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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