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30f72e2482
* Making the output from the VEP-moduel (ENSEMBLVEP) optionally vcf, json or tab. #1774 * Trying to fix tests * Still trying to fix tests * Fetching the vep-output-file-extension from the args. * Update meta.yml * WIP: Adding tests for vep-output json and tab * updated the test.yml Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: nvnieuwk <nicolas.vannieuwkerke@ugent.be>
39 lines
1.6 KiB
YAML
39 lines
1.6 KiB
YAML
- name: ensemblvep test_ensemblvep_fasta_json
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command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_json -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
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tags:
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- ensemblvep
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files:
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- path: output/ensemblvep/test.ann.json
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- path: output/ensemblvep/test.summary.html
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- name: ensemblvep test_ensemblvep_fasta_tab
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command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_tab -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
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tags:
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- ensemblvep
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files:
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- path: output/ensemblvep/test.ann.tab
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- path: output/ensemblvep/test.summary.html
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- name: ensemblvep test_ensemblvep_fasta_vcf
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command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_vcf -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
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tags:
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- ensemblvep
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files:
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- path: output/ensemblvep/test.ann.vcf
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- path: output/ensemblvep/test.summary.html
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- name: ensemblvep test_ensemblvep_fasta
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command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
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tags:
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- ensemblvep
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files:
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- path: output/ensemblvep/test.ann.vcf
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- path: output/ensemblvep/test.summary.html
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- name: ensemblvep test_ensemblvep_no_fasta
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command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_no_fasta -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
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tags:
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- ensemblvep
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files:
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- path: output/ensemblvep/test.ann.vcf
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- path: output/ensemblvep/test.summary.html
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