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Add vcfpgloader/load module (nf-core#9579)
* Add vcfpgloader/load module High-throughput VCF to PostgreSQL loader using asyncpg for bulk variant ingestion. * Remove throughput metric from meta.yml description * fix(vcfpgloader): fix CI failures for conda, singularity, and docker - Add pip as explicit conda dependency in environment.yml - Simplify container directive (remove oras:// for singularity compatibility) - Remove integration test requiring PostgreSQL database 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> * chore: re-trigger CI for bioconda 0.5.3 propagation * chore: reorder deps to bust conda cache for 0.5.3 * fix: specify exact bioconda build string to force 0.5.3 * chore: sort environment.yml dependencies (linter) * fix: remove version from snapshot (varies by profile) * fix(vcfpgloader): restore version checking in tests Add back versions to snapshot assertions and update snapshot file with expected version output format for lint compliance. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> * fix(vcfpgloader): use correct findAll pattern for topic versions Use process.out.findAll { key, val -> key.startsWith("versions")} pattern for topic-based versioning, matching nf-core conventions. Update snapshot with versions_vcfpgloader object format. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> * feat(vcfpgloader): bump to v0.5.4 - Update environment.yml to bioconda::vcf-pg-loader=0.5.4 - Update container to ghcr.io/zacharyr41/vcf-pg-loader:0.5.4 - Add sed to parse version number from --version output - Update snapshot for 0.5.4 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> * ci: retrigger after bioconda 0.5.4 merge * fix(vcfpgloader): update meta.yml version format Add type: eval and description to version command entries in outputs and topics sections. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]> * style(vcfpgloader): apply nextflow lint formatting * fix(vcfpgloader): add export to env() output variables Add explicit `export` to ROWS_LOADED assignments as recommended for env() output qualifiers. Note: `nextflow lint` still reports false positive errors for env() outputs - this is a known limitation of static analysis on shell scripts. The linter cannot verify variable definitions inside heredoc script blocks. Other nf-core modules (e.g., genescopefk) have the same lint warning. The code functions correctly at runtime. * Update modules/nf-core/vcfpgloader/load/tests/nextflow.config Co-authored-by: Famke Bäuerle <[email protected]> * chore(vcfpgloader): remove unused tags.yml * Update modules/nf-core/vcfpgloader/load/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/vcfpgloader/load/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * refactor(vcfpgloader): consolidate inputs into single tuple * feat(vcfpgloader): switch to BioContainers - Use BioContainers URLs instead of personal ghcr.io - Remove jq dependency, use Python for JSON parsing - Fix sed quoting for nf-core lint compatibility 🤖 Generated with [Claude Code](https://claude.ai/code) * fix(vcfpgloader): update snapshots to include row_count output Add missing row_count and log outputs to test snapshots to match the process outputs being asserted in tests. --------- Co-authored-by: Claude <[email protected]> Co-authored-by: Zachary Rothstein <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]>
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‎modules/nf-core/vcfpgloader/load/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- bioconda::vcf-pg-loader=0.5.4

‎modules/nf-core/vcfpgloader/load/main.nf‎

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// Database connection parameters are passed as val() inputs to support
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// dynamic per-sample configuration. Set PGPASSWORD via environment variable
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// or Nextflow secrets before running:
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//
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// Option 1 - Environment variable:
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// export PGPASSWORD='your_password'
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//
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// Option 2 - Nextflow secrets (nextflow.config):
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// env {
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// PGPASSWORD = secrets.PGPASSWORD
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// }
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process VCFPGLOADER_LOAD {
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tag "${meta.id}"
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label 'process_medium'
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/vcf-pg-loader:0.5.4--pyhdfd78af_0' :
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'biocontainers/vcf-pg-loader:0.5.4--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(vcf), path(tbi), val(db_host), val(db_port), val(db_name), val(db_user), val(db_schema)
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output:
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tuple val(meta), path("*.load_report.json"), emit: report
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tuple val(meta), path("*.load.log"), emit: log
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tuple val(meta), env(ROWS_LOADED), emit: row_count
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tuple val("${task.process}"), val("vcf-pg-loader"), eval("vcf-pg-loader --version | sed 's/.*version //'"), topic: versions, emit: versions_vcfpgloader
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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// NOTE: batch_size exposed via task.ext for pipeline-level tuning of memory/performance tradeoffs
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def batch_size = task.ext.batch_size ?: '10000'
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"""
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vcf-pg-loader load \\
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--host ${db_host} \\
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--port ${db_port} \\
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--database ${db_name} \\
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--user ${db_user} \\
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--schema ${db_schema} \\
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--batch ${batch_size} \\
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--workers ${task.cpus} \\
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--sample-id ${meta.id} \\
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--report ${prefix}.load_report.json \\
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--log ${prefix}.load.log \\
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${args} \\
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${vcf}
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export ROWS_LOADED=\$(python3 -c "import json; print(json.load(open('${prefix}.load_report.json'))['variants_loaded'])")
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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cat <<-END_JSON > ${prefix}.load_report.json
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{"status": "stub", "variants_loaded": 0, "elapsed_seconds": 0}
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END_JSON
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touch ${prefix}.load.log
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export ROWS_LOADED=0
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"""
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}

‎modules/nf-core/vcfpgloader/load/meta.yml‎

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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name: "vcfpgloader_load"
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description: High-performance VCF to PostgreSQL loader using asyncpg for bulk
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variant ingestion
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keywords:
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- vcf
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- postgresql
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- database
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- variants
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- genomics
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- clinical
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- annotation
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tools:
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- vcf-pg-loader:
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description: |
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High-throughput async PostgreSQL VCF loader using cyvcf2 and asyncpg.
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Supports variant normalization, multi-allelic decomposition, and clinical-grade audit trails.
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homepage: "https://github.com/Zacharyr41/vcf-pg-loader"
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documentation: "https://github.com/Zacharyr41/vcf-pg-loader#readme"
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tool_dev_url: "https://github.com/Zacharyr41/vcf-pg-loader"
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licence: ["MIT"]
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identifier: ""
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args_id: "$args"
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'sample1', family:'FAM001', affected:true ]
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- vcf:
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type: file
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description: Annotated VCF file containing variants to load
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pattern: "*.{vcf,vcf.gz}"
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ontologies:
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- edam: "http://edamontology.org/format_3016"
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- tbi:
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type: file
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description: Tabix index for the VCF file
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pattern: "*.tbi"
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ontologies: []
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- db_host:
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type: string
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description: PostgreSQL server hostname or IP address
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- db_port:
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type: integer
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description: PostgreSQL server port (default 5432)
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- db_name:
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type: string
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description: Target database name
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- db_user:
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type: string
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description: Database username for authentication
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- db_schema:
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type: string
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description: Target schema for variant tables (default public)
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output:
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report:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'sample1' ]
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- "*.load_report.json":
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type: file
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description: JSON report with loading statistics including variant
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counts, elapsed time, and throughput metrics
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pattern: "*.load_report.json"
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ontologies:
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- edam: "http://edamontology.org/format_3464"
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log:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'sample1' ]
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- "*.load.log":
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type: file
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description: Detailed loading log with any warnings or errors
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pattern: "*.load.log"
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ontologies:
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- edam: "http://edamontology.org/format_2330"
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row_count:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'sample1' ]
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- ROWS_LOADED:
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type: integer
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description: Number of variant records successfully loaded
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versions_vcfpgloader:
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- - ${task.process}:
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type: string
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description: The name of the process
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- vcf-pg-loader:
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type: string
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description: The name of the tool
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- "vcf-pg-loader --version | sed 's/.*version //'":
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type: eval
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description: The expression to obtain the version of the tool
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topics:
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versions:
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- - ${task.process}:
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type: string
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description: The name of the process
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- vcf-pg-loader:
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type: string
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description: The name of the tool
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- "vcf-pg-loader --version | sed 's/.*version //'":
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type: eval
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description: The expression to obtain the version of the tool
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authors:
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- "@Zacharyr41"
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maintainers:
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- "@Zacharyr41"

‎modules/nf-core/vcfpgloader/load/tests/main.nf.test‎

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nextflow_process {
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name "Test Process VCFPGLOADER_LOAD"
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script "../main.nf"
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process "VCFPGLOADER_LOAD"
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config "./nextflow.config"
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tag "modules"
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tag "modules_nfcore"
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tag "vcfpgloader"
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tag "vcfpgloader/load"
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tag "database"
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test("sarscov2 - vcf.gz - stub") {
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tag "stub"
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options "-stub"
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when {
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process {
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"""
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input[0] = [
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[ id: 'test_sample', family: 'TEST_FAM' ],
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
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'localhost',
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5432,
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'testdb',
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'postgres',
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'public'
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]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(
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process.out.report,
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process.out.log,
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process.out.row_count,
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process.out.findAll { key, val -> key.startsWith("versions")}
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).match() }
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)
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}
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}
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test("homo_sapiens - gatk vcf.gz - stub") {
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tag "stub"
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options "-stub"
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when {
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process {
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"""
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input[0] = [
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[ id: 'test_human' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotc.vcf.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotc.vcf.gz.tbi', checkIfExists: true),
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'localhost',
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5432,
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'testdb',
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'postgres',
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'public'
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]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(
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process.out.report,
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process.out.log,
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process.out.row_count,
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process.out.findAll { key, val -> key.startsWith("versions")}
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).match() }
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)
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}
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}
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}

‎modules/nf-core/vcfpgloader/load/tests/main.nf.test.snap‎

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{
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"homo_sapiens - gatk vcf.gz - stub": {
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"content": [
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[
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[
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{
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"id": "test_human"
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},
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"test_human.load_report.json:md5,0c600325e85cdf50ee557916606fe2b1"
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]
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],
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[
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[
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{
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"id": "test_human"
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},
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"test_human.load.log:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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[
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[
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{
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"id": "test_human"
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},
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"0"
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]
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],
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{
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"versions_vcfpgloader": [
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[
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"VCFPGLOADER_LOAD",
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"vcf-pg-loader",
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"0.5.4"
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]
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]
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}
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.2"
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},
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"timestamp": "2025-12-25T18:30:00.000000"
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},
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"sarscov2 - vcf.gz - stub": {
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"content": [
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[
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[
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{
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"id": "test_sample",
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"family": "TEST_FAM"
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},
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"test_sample.load_report.json:md5,0c600325e85cdf50ee557916606fe2b1"
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]
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],
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[
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[
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{
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"id": "test_sample",
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"family": "TEST_FAM"
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},
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"test_sample.load.log:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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[
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[
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{
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"id": "test_sample",
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"family": "TEST_FAM"
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},
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"0"
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]
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],
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{
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"versions_vcfpgloader": [
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[
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"VCFPGLOADER_LOAD",
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"vcf-pg-loader",
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"0.5.4"
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]
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]
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}
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.2"
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},
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"timestamp": "2025-12-25T18:30:00.000000"
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}
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}

‎modules/nf-core/vcfpgloader/load/tests/nextflow.config‎

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env {
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PGPASSWORD = 'test_password'
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}
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process {
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withName: 'VCFPGLOADER_LOAD' {
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ext.args = ''
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ext.batch_size = '10000'
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}
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}

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