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661bdb645e
* Change spades module * correct meta map description * adjust memory handling * remove trailing whitespace * fix hmm input * Update modules/spades/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
48 lines
1.8 KiB
Text
48 lines
1.8 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SPADES } from '../../../modules/spades/main.nf' addParams( options: ['args': '--rnaviral'] )
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workflow test_spades_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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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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]
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SPADES ( input, [] )
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}
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workflow test_spades_paired_end {
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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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[]
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]
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SPADES ( input, [] )
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}
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workflow test_spades_illumina_nanopore {
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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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[ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
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]
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SPADES ( input, [] )
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}
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// that isnt perfect, because CCS reads should rather be used with -s instead of --pacbio
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workflow test_spades_illumina_pacbio {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
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[ file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true) ],
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[]
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]
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SPADES ( input, [] )
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}
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