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f079367416
* Building Picard liftovervcf module * Building Picard liftovervcf module_test * Building Picard liftovervcf pytest * Module for picard liftover vcf created * Fixed files after linting test * Fixed trailing whitespace * Checked files with prettier * further formatting with prettier * Fixed test.yml * Fixed input variable names * Changed contain test.liftef.vcf * Changed contain in test.yml test.liftef.vcf * Run prittier * Going back to previous version of test.yml * downgrading picard to 2.26.10 from 2.26.11 * Update modules/picard/liftovervcf/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/liftovervcf/main.nf Print available memory Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Output from .vcf to .vcf.gz * Added spaces to align emit * Update modules/picard/liftovervcf/meta.yml Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/liftovervcf/meta.yml Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/liftovervcf/meta.yml Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Removing md5sum test Co-authored-by: jemten <jemten@users.noreply.github.com> Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
17 lines
680 B
Text
17 lines
680 B
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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