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f126d980d7
* inital commit * added meta.yaml info * add initial logic for featurecounts test * add args and change SE/PE to strandedness for featurecounts test * added tests to pytest * added test.yml * removed GTF flag in options * corrected test meta params * meta yaml corrected tool info * update test.yml * fix lint errors meta.yml Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
35 lines
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1.3 KiB
Text
35 lines
No EOL
1.3 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SUBREAD_FEATURECOUNTS } from '../../../../software/subread/featurecounts/main.nf' addParams( options: [args:'-t CDS'] )
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workflow test_subread_featurecounts_forward {
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def input = []
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input = [ [ id:'test', single_end:true, strandedness:'forward' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
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SUBREAD_FEATURECOUNTS ( input )
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}
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workflow test_subread_featurecounts_reverse {
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def input = []
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input = [ [ id:'test', single_end:true, strandedness:'reverse' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
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SUBREAD_FEATURECOUNTS ( input )
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}
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workflow test_subread_featurecounts_unstranded {
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def input = []
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input = [ [ id:'test', single_end:true, strandedness:'unstranded' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) ]
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SUBREAD_FEATURECOUNTS ( input )
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} |