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41 lines
1.6 KiB
Text
41 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { DEEPTOOLS_BAMCOVERAGE } from '../../../../modules/deeptools/bamcoverage/main.nf'
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workflow test_deeptools_bamcoverage_bam {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
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]
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DEEPTOOLS_BAMCOVERAGE ( input, [], [] )
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}
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workflow test_deeptools_bamcoverage_cram {
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input = [
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[ id:'test', single_end:false ], // 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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fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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DEEPTOOLS_BAMCOVERAGE ( input, fasta, fasta_fai)
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}
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workflow test_deeptools_bamcoverage_cram_no_fasta_fai {
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input = [
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[ id:'test', single_end:false ], // 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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DEEPTOOLS_BAMCOVERAGE ( input, fasta, [])
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}
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