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49 lines
2 KiB
Text
49 lines
2 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BISCUIT_INDEX } from '../../../../modules/biscuit/index/main.nf'
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include { BISCUIT_EPIREAD } from '../../../../modules/biscuit/epiread/main.nf'
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workflow test_biscuit_epiread_nosnp {
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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_methylated_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
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[] //SNP BED file
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BISCUIT_INDEX( fasta )
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BISCUIT_EPIREAD ( input, BISCUIT_INDEX.out.index )
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}
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workflow test_biscuit_epiread_snp {
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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_methylated_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
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file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed')
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BISCUIT_INDEX( fasta )
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BISCUIT_EPIREAD ( input, BISCUIT_INDEX.out.index )
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}
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workflow test_biscuit_epiread_snp_decompress {
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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_methylated_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
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file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed.gz')
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BISCUIT_INDEX( fasta )
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BISCUIT_EPIREAD ( input, BISCUIT_INDEX.out.index )
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}
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