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Fixed VEP s3 bucket path #127

Merged
merged 2 commits into from
Feb 15, 2024
Merged

Fixed VEP s3 bucket path #127

merged 2 commits into from
Feb 15, 2024

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nschcolnicov
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@nschcolnicov nschcolnicov commented Feb 15, 2024 •
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The issue is described here: #126

I tested it with the command:
nextflow run ../../main.nf -profile docker -c config.config --outdir . --annotate_tools merge -resume
image

The config.config file contains the same values as the test profile but without the snpeff_cache and vep_cache being set to null:

params {
    config_profile_name        = 'Test profile'
    config_profile_description = 'Minimal test dataset to check pipeline function'

    // Limit resources so that this can run on GitHub Actions
    max_cpus   = 2
    max_memory = '6.GB'
    max_time   = '6.h'

    // Input data
    input = "${projectDir}/tests/csv/1.0/fastq_single.csv"

    // Genome references
    genome              = 'WBcel235'
    fasta               = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
    dict                = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.dict'
    gtf                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.gtf'

    // Known genome resources (optional)
    dbsnp               = 'https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz'
    dbsnp_tbi           = 'https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi'
    known_indels        = 'https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz'
    known_indels_tbi    = 'https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi'

    // STAR index (optional)
    star_index          = 'https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/index/star/star.tar.gz'

    // Annotation
    snpeff_db         = 105
    snpeff_genome     = 'WBcel235'
    vep_cache_version = 110
    vep_genome        = 'WBcel235'
    vep_species       = 'caenorhabditis_elegans'
}

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/rnavar branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

@nschcolnicov nschcolnicov mentioned this pull request Feb 15, 2024
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github-actions bot commented Feb 15, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3de9b74

+| ✅ 188 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in WorkflowRnavar.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-15 14:05:07

@maxulysse maxulysse merged commit d47e3ff into nf-core:dev Feb 15, 2024
12 checks passed
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@maxulysse maxulysse maxulysse approved these changes

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@nschcolnicov @maxulysse