Fix/clinvar prepare #206
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| Original file line number | Diff line number | Diff line change |
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| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| # renovate: datasource=conda depName=conda-forge/wget | ||
| - conda-forge::wget=1.21.4 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,68 @@ | ||
| process VEPPLUGIN_CLINVAR { | ||
| tag "${vcf_url.toString().tokenize('/').last()}" | ||
| label 'process_single' | ||
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| conda "${moduleDir}/environment.yml" | ||
| container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container | ||
| ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3b/3b54fa9135194c72a18d00db6b399c03248103f87e43ca75e4b50d61179994b3/data' | ||
| : 'community.wave.seqera.io/library/wget:1.21.4--8b0fcde81c17be5e'}" | ||
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| input: | ||
| tuple val(vcf_url), val(tbi_url), val(md5), val(tbi_md5) | ||
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| output: | ||
| path "${vcf_name}{,.tbi}", emit: files | ||
| // versions.yml rather than an eval() topic: eval outputs are numbered pipeline-wide, so adding | ||
| // one shifts the cache key of every other task that has one and breaks -resume of existing runs | ||
| path "versions.yml" , emit: versions | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| def args = task.ext.args ?: '' | ||
| vcf_name = vcf_url.toString().tokenize('/').last() | ||
| def sums = [ md5 ? "${md5} ${vcf_name}" : null, tbi_md5 ? "${tbi_md5} ${vcf_name}.tbi" : null ].findAll() | ||
| def check = sums ? "printf '%s\\n' ${sums.collect { line -> "'${line}'" }.join(' ')} | md5sum -c -" : '' | ||
| """ | ||
| # Retry a transient 503 from NCBI: a linear backoff of 1 s, 2 s, ... up to 10 s, about 45 s over 10 tries | ||
| wget \\ | ||
| --no-verbose \\ | ||
| --tries=10 \\ | ||
| --waitretry=10 \\ | ||
| --retry-on-http-error=429,500,502,503,504 \\ | ||
| ${args} \\ | ||
| -O ${vcf_name} \\ | ||
| ${vcf_url} | ||
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| # Saved next to the VCF under the name VEP looks for, whatever the host calls it | ||
| wget \\ | ||
| --no-verbose \\ | ||
| --tries=10 \\ | ||
| --waitretry=10 \\ | ||
| --retry-on-http-error=429,500,502,503,504 \\ | ||
| ${args} \\ | ||
| -O ${vcf_name}.tbi \\ | ||
| ${tbi_url} | ||
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| # Pinned checksums keep the release fixed: a host that re-publishes under the same name fails here | ||
| ${check} | ||
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| wget: \$(wget --version | head -1 | cut -d ' ' -f 3) | ||
| END_VERSIONS | ||
| """ | ||
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| stub: | ||
| vcf_name = vcf_url.toString().tokenize('/').last() | ||
| """ | ||
| echo "" | gzip > ${vcf_name} | ||
| touch ${vcf_name}.tbi | ||
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| wget: \$(wget --version | head -1 | cut -d ' ' -f 3) | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: "vepplugin_clinvar" | ||
| description: Download a dated ClinVar VCF and its index once per run, checked against a pinned MD5, for the VEP --custom annotation | ||
| keywords: | ||
| - vep | ||
| - clinvar | ||
| - download | ||
| - annotation | ||
| tools: | ||
| - "wget": | ||
| description: "GNU Wget is a free software package for retrieving files using HTTP, HTTPS, FTP and FTPS" | ||
| homepage: "https://www.gnu.org/software/wget/" | ||
| documentation: "https://www.gnu.org/software/wget/manual/wget.html" | ||
| licence: ["GPL-3.0-or-later"] | ||
| identifier: "" | ||
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| input: | ||
| - - vcf_url: | ||
| type: string | ||
| description: URL of the ClinVar VCF; its basename becomes the output name | ||
| - tbi_url: | ||
| type: string | ||
| description: URL of the tabix index published alongside the VCF | ||
| - md5: | ||
| type: string | ||
| description: | | ||
| Expected MD5 of the VCF. When set, a download that does not match fails | ||
| the task. May be null, in which case the release is not verified. | ||
| - tbi_md5: | ||
| type: string | ||
| description: | | ||
| Expected MD5 of the index, checked the same way. May be null, as for | ||
| NCBI, which publishes no checksum for its indexes. | ||
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| output: | ||
| files: | ||
| - "${vcf_name}{,.tbi}": | ||
| type: file | ||
| description: The ClinVar VCF and its tabix index | ||
| pattern: "*.vcf.gz{,.tbi}" | ||
| versions: | ||
| - versions.yml: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
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| authors: | ||
| - "@AmberVerhasselt" | ||
| maintainers: | ||
| - "@AmberVerhasselt" |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,41 @@ | ||
| nextflow_process { | ||
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| name "Test Process VEPPLUGIN_CLINVAR" | ||
| script "../main.nf" | ||
| process "VEPPLUGIN_CLINVAR" | ||
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| // "small" is what .github/workflows/nf-test.yml selects on for pull_request | ||
| tag "small" | ||
| tag "modules" | ||
| tag "modules_local" | ||
| tag "vepplugin_clinvar" | ||
|
Collaborator
There was a problem hiding this comment. Nit: PR CI runs only |
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| // Stub only: a real run downloads the full ClinVar release | ||
| test("clinvar release - stub") { | ||
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| options "-stub" | ||
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| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| 'https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2026/clinvar_20260829.vcf.gz', | ||
| 'https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2026/clinvar_20260829.vcf.gz.tbi', | ||
| 'dffae274fd559ee764d1de44f36df2cf', | ||
| null // NCBI publishes no checksum for its index | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assert process.success | ||
| assertAll( | ||
| // the VCF keeps its release name, and the index sits beside it under the name VEP looks for | ||
| { assert process.out.files[0].collect { f -> file(f).name }.sort() == [ 'clinvar_20260829.vcf.gz', 'clinvar_20260829.vcf.gz.tbi' ] }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
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| } | ||
| } | ||
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This block replaces the default
publishDir, and the default is where thesaveAsthat dropsversions.ymllives. REVEL and EVE report their versions through topics, so this never mattered for them.VEPPLUGIN_CLINVARemits aversions.yml, so every run now publishes<outdir>/vep_plugins/versions.yml.