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83 lines
3 KiB
Text
83 lines
3 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { UMITOOLS_EXTRACT } from '../../../../modules/umitools/extract/main.nf'
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include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
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include { BWA_MEM } from '../../../../modules/bwa/mem/main.nf'
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include { SAMTOOLS_INDEX } from '../../../../modules/samtools/index/main.nf'
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include { UMITOOLS_DEDUP } from '../../../../modules/umitools/dedup/main.nf'
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//
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// Test with no UMI
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//
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workflow test_umitools_dedup_no_umi {
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input = [
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[ id:'test'], // 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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get_output_stats = false
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UMITOOLS_DEDUP ( input, get_output_stats )
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}
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//
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// Test with single-end data without --output-stats
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//
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workflow test_umitools_dedup_single_end_no_stats {
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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_1_fastq_gz'], 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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get_output_stats = false
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UMITOOLS_EXTRACT ( input )
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BWA_INDEX ( fasta )
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BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
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SAMTOOLS_INDEX ( BWA_MEM.out.bam )
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UMITOOLS_DEDUP ( BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), get_output_stats )
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}
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//
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// Test with paired-end data without --output-stats
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//
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workflow test_umitools_dedup_paired_end_no_stats {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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get_output_stats = false
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UMITOOLS_EXTRACT ( input )
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BWA_INDEX ( fasta )
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BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
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SAMTOOLS_INDEX ( BWA_MEM.out.bam )
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UMITOOLS_DEDUP ( BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), get_output_stats )
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}
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//
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// Test with paired-end data with --output-stats
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//
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workflow test_umitools_dedup_paired_end_stats {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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get_output_stats = true
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UMITOOLS_EXTRACT ( input )
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BWA_INDEX ( fasta )
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BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
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SAMTOOLS_INDEX ( BWA_MEM.out.bam )
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UMITOOLS_DEDUP ( BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), get_output_stats )
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}
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