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29 lines
1.2 KiB
Text
29 lines
1.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SAMTOOLS_MERGE } from '../../../../modules/samtools/merge/main.nf'
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workflow test_samtools_merge {
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input = [ [ id: 'test' ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
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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_single_end_sorted_bam'], checkIfExists: true)
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]
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]
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SAMTOOLS_MERGE ( input, [], [] )
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}
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workflow test_samtools_merge_cram {
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input = [ [ id: 'test' ], // meta map
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[
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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']['test2_paired_end_recalibrated_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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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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SAMTOOLS_MERGE ( input, fasta, fai )
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}
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