Remove duplicate input causing test profile to fail

[madhavajay]

Hi,
I tried running this:

nextflow run nf-core/raredisease -revision 2.5.0 -profile test --outdir /home/azureuser/debug/

I got:

Workflow `NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS` declares 14 input channels but 13 were given

ANNOTATE_MT_SNVS (
    CALL_SNV.out.mt_vcf,
    CALL_SNV.out.mt_tabix,
    ch_cadd_header,
    ch_cadd_resources,
    ch_genome_fasta,
    ch_vcfanno_extra,
    ch_vcfanno_lua,
    ch_vcfanno_resources,
    ch_vcfanno_toml,
    params.genome,
    params.vep_cache_version,
    ch_vep_cache,
    ch_vep_extra_files
).set { ch_mt_annotate }

But the file I have looked at has ch_vep_cache twice.

I haven't setup the local dev tools yet but I will when I get a moment.

Chat here:
https://nfcore.slack.com/archives/C025UH66DA8/p1749004714662999

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[ramprasadn]

Hi @madhavajay! Thanks for your PR. We actually noticed the duplicate entry a couple of weeks ago, and the fix has already been merged into our dev branch. Could you switch the version from 2.5.0 to dev and check if the issue persists?

Alternatively, you can also try running the master branch with Nextflow versions 24.10.x, which should resolve the issue.

[madhavajay]

Hi @ramprasadn oh no problem that makes sense, will that also help us with this issue:

params.vcfanno_resources not set.
params.vcfanno_toml not set.
params.vep_cache not set.
params.gnomad_af not set.
params.score_config_snv not set.
params.variant_consequences_snv not set.
params.score_config_sv not set.
params.variant_consequences_sv not set.
params.ploidy_model not set.
params.gcnvcaller_model not set.
params.readcount_intervals not set.
params.mobile_element_references not set.
params.mobile_element_svdb_annotations not set.

Im trying to run some kind of basic example of nf-core/raredisease but I can't find a clear tutorial. Is there some data we need to run it?

I ran nextflow/sarek without any issue like this:

nextflow run nf-core/sarek \
  -r 3.5.1 \
  -profile docker \
  --input ./samplesheet.csv \
  --outdir ./results \
  --genome GATK.GRCh38 \
  --tools manta,strelka,tiddit,vep,snpeff,controlfreec \
  --step mapping

Do you know what I would need to do differently?