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826a5603db
* Stage fastq for concat in subfolders in task workdir * Update main.nf * Update test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
49 lines
1.8 KiB
Text
49 lines
1.8 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { CAT_FASTQ } from '../../../../modules/cat/fastq/main.nf'
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workflow test_cat_fastq_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_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ]
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]
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CAT_FASTQ ( input )
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}
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workflow test_cat_fastq_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_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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file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ]
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]
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CAT_FASTQ ( input )
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}
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workflow test_cat_fastq_single_end_same_name {
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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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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
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]
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CAT_FASTQ ( input )
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}
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workflow test_cat_fastq_paired_end_same_name {
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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_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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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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CAT_FASTQ ( input )
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}
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