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f434d0c671
* feat added stubs to picard_liftovervcf * feat adding stubs to gatk4_mergevcfs * feat adding stubs to gatk4_filtermutectcalls * fix tests * fix output name filtermutectcalls * fix test * fix added missing [ * Update tests/modules/gatk4/mergevcfs/test.yml Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update tests/modules/gatk4/filtermutectcalls/test.yml Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update tests/modules/picard/liftovervcf/test.yml Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/filtermutectcalls/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/filtermutectcalls/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/mergevcfs/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/mergevcfs/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/picard/liftovervcf/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Trying something on picard_liftovervcf * fix adding test data for stubs * fix added bracket and unindented workflow * fix picard 2.27.1 -> 2.27.0 to solve PaddingError * Update main.nf fix added tbi to stub Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
21 lines
771 B
YAML
21 lines
771 B
YAML
- name: picard liftovervcf test_picard_liftovervcf
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command: nextflow run tests/modules/picard/liftovervcf -entry test_picard_liftovervcf -c tests/config/nextflow.config
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tags:
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- picard/liftovervcf
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- picard
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files:
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- path: output/picard/test.lifted.vcf.gz
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contains:
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- "chr22"
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- path: output/picard/test.unlifted.vcf.gz
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- path: output/picard/versions.yml
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- name: picard liftovervcf test_picard_liftovervcf_stubs
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command: nextflow run tests/modules/picard/liftovervcf -entry test_picard_liftovervcf_stubs -c tests/config/nextflow.config -stub-run
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tags:
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- picard/liftovervcf
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- picard
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files:
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- path: output/picard/test.lifted.vcf.gz
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- path: output/picard/test.unlifted.vcf.gz
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- path: output/picard/versions.yml
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