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https://github.com/MillironX/nf-core_modules.git
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d1c6082a66
* Update HISAT2 build module * Bump preseq version * Fix tests * Add meta.yml for preseq to fix linting * Auto-detect --genomeSAindexNbases for smaller genomes * Add placeholder to use human data for the tests * Add CSI output option to samtools/index * Fix samtools/index tests
22 lines
828 B
Text
22 lines
828 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_BAI } from '../../../../software/samtools/index/main.nf' addParams( options: [:] )
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include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CSI } from '../../../../software/samtools/index/main.nf' addParams( options: [args:'-c'] )
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workflow test_samtools_index_bai {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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SAMTOOLS_INDEX_BAI ( input )
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}
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workflow test_samtools_index_csi {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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SAMTOOLS_INDEX_CSI ( input )
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}
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