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09159edc9e
* samtools view update * remove csi output * prettier * update meta * add index functionality * prettier * fixed test checks
53 lines
1.8 KiB
Text
53 lines
1.8 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SAMTOOLS_VIEW } from '../../../../modules/samtools/view/main.nf'
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workflow test_samtools_view {
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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_bam'], checkIfExists: true),
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[]
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]
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SAMTOOLS_VIEW ( input, [] )
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}
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workflow test_samtools_view_cram {
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input = [ [ id: 'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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SAMTOOLS_VIEW ( input, fasta )
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}
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workflow test_samtools_view_convert {
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input = [ [ id: 'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
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[]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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SAMTOOLS_VIEW ( input, fasta )
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}
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workflow test_samtools_view_index {
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input = [ [ id: 'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
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[]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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SAMTOOLS_VIEW ( input, fasta )
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}
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workflow test_samtools_view_stubs {
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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_bam'], checkIfExists: true),
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[]
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]
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SAMTOOLS_VIEW ( input, [] )
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}
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