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83b05a8dc0
* add qname feature to samtools_view * update tests * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * added filter tests Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
65 lines
2.3 KiB
Text
65 lines
2.3 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_filter {
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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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qname = Channel.of("testN:2817", "testN:2814").collectFile(name: "readnames.list", newLine: true)
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SAMTOOLS_VIEW ( input, fasta, qname )
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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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