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29 lines
1.2 KiB
Plaintext
29 lines
1.2 KiB
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BAM_STATS_SAMTOOLS as BAM_STATS_SAMTOOLS_SINGLE_END } from '../../../../subworkflows/nf-core/bam_stats_samtools/main'
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include { BAM_STATS_SAMTOOLS as BAM_STATS_SAMTOOLS_PAIRED_END } from '../../../../subworkflows/nf-core/bam_stats_samtools/main'
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workflow test_bam_stats_samtools_single_end {
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input = [
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[ id:'test', single_end:true ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BAM_STATS_SAMTOOLS_SINGLE_END ( input, fasta )
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}
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workflow test_bam_stats_samtools_paired_end {
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input = [
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[ 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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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BAM_STATS_SAMTOOLS_PAIRED_END ( input, fasta )
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}
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