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32 lines
1.4 KiB
Text
32 lines
1.4 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM } from '../../../../modules/samtools/convert/main.nf'
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include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM } from '../../../../modules/samtools/convert/main.nf'
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workflow test_samtools_convert_bamtocram {
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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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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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SAMTOOLS_BAMTOCRAM ( input, fasta, fai )
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}
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workflow test_samtools_convert_cramtobam {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_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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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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SAMTOOLS_CRAMTOBAM ( input, fasta, fai )
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}
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