Update pb deepvariant #7363
Update pb deepvariant #7363
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| @@ -44,9 +50,15 @@ nextflow_process { | |||
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| test("human - bam - intervals") { | |||
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| config './nextflow.config' | |||
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If this is now added to all tests we can also move it to the top of the file avoiding too much code duplication :)
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yes good idea - we can do that! This seemed to be the pattern used in other module tests, but happy to adjust!
| tuple val(ref_meta), path(fasta) | ||
| path model_file |
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Can you also include a test that uses this model file?
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yes good idea - @gburnett-nvidia and I will find a model file and add a test. Will have to also find a way to host the model file... somewhere.
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the model file can go into nf-core/test-datasets
| tuple val(meta), path("*.vcf"), optional: true, emit: vcf | ||
| tuple val(meta), path("*.g.vcf"), optional: true, emit: gvcf | ||
| path "versions.yml", emit: versions |
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Can you align these nicely? (as it was before)
| tuple val(meta), path("*.vcf"), optional: true, emit: vcf | ||
| tuple val(meta), path("*.g.vcf"), optional: true, emit: gvcf |
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Is there a possibility to return gzipped vcf files as standard?
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Right now there is no way for Parabricks directly to return gzipped vcf files. It would have to be added as an additional step.
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Maye you can add bgzip to the parabricks docker/singularity container? Then we could easily do it in the script section of the module. That would be very helpful!
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PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda