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e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
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 '../../../../modules/seqkit/split2/main.nf' addParams( options: ['args': '--by-length 8K'] )
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include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../modules/seqkit/split2/main.nf' addParams( options: ['args': '--by-size 50' ] )
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include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../modules/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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