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86df111707
* Update test path * Fix bracket Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
58 lines
2.3 KiB
Text
58 lines
2.3 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../software/seqkit/split2/main.nf' addParams( options: ['args': '--by-length 8K'] )
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include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../software/seqkit/split2/main.nf' addParams( options: ['args': '--by-size 50' ] )
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include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../software/seqkit/split2/main.nf' addParams( options: ['args': '--by-part 3'] )
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workflow test_seqkit_split2_single_end_length {
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input = [ [ 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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SEQKIT_SPLIT2_LENGTH ( input )
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}
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workflow test_seqkit_split2_single_end_size {
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input = [ [ 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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SEQKIT_SPLIT2_SIZE ( input )
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}
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workflow test_seqkit_split2_single_end_part {
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input = [ [ 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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SEQKIT_SPLIT2_PART ( input )
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}
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workflow test_seqkit_split2_paired_end_length {
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input = [ [ 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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]
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SEQKIT_SPLIT2_LENGTH ( input )
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}
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workflow test_seqkit_split2_paired_end_size {
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input = [ [ 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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]
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SEQKIT_SPLIT2_SIZE ( input )
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}
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workflow test_seqkit_split2_paired_end_part {
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input = [ [ 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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]
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SEQKIT_SPLIT2_PART ( input )
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}
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