Test data is not available
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- Dominant language
- Nextflow
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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
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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