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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>
29 lines
1.2 KiB
Text
29 lines
1.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { PICARD_LIFTOVERVCF } from '../../../../modules/picard/liftovervcf/main.nf'
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workflow test_picard_liftovervcf {
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input_vcf = [ [ id:'test' ],
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
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]
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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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chain = file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
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fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
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PICARD_LIFTOVERVCF ( input_vcf, dict, chain, fasta )
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}
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workflow test_picard_liftovervcf_stubs {
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input_vcf = [ [ id:'test' ],
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
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]
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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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chain = file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
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fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
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PICARD_LIFTOVERVCF ( input_vcf, dict, chain, fasta )
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}
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