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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>
35 lines
1.2 KiB
Text
35 lines
1.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_MERGEVCFS } from '../../../../modules/gatk4/mergevcfs/main.nf'
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workflow test_gatk4_mergevcfs {
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def input = []
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
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]
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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GATK4_MERGEVCFS ( input, dict )
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}
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workflow test_gatk4_mergevcfs_no_dict {
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
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]
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GATK4_MERGEVCFS ( input, [] )
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}
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workflow test_gatk4_mergevcfs_no_dict_stubs {
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
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]
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GATK4_MERGEVCFS ( input, [] )
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}
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