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52c541b080
* rebuild cooler cload. * update test file path of cload. * add pytest for cload * update to version.yml * update the test data path * Update tests/modules/cooler/cload/main.nf Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * Update modules/cooler/cload/main.nf Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * Update tests/config/test_data.config Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * Update main.nf Remove a lonely curly bracket. * Update test.yml Updated with new workflows. * update the test files * merge the conflicts. * update the test.yml * update for change of cooler/dump Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
52 lines
2.4 KiB
Text
52 lines
2.4 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { COOLER_CLOAD } from '../../../../modules/cooler/cload/main.nf' addParams( options: [args:'pairix'] )
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include { COOLER_CLOAD as COOLER_CLOAD_PAIRS } from '../../../../modules/cooler/cload/main.nf' addParams( options: [args:'pairs --chrom1 1 --pos1 2 --chrom2 4 --pos2 5 -N'] )
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include { COOLER_CLOAD as COOLER_CLOAD_TABIX } from '../../../../modules/cooler/cload/main.nf' addParams( options: [args:'tabix'] )
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include { COOLER_DUMP } from '../../../../modules/cooler/dump/main.nf' addParams( options: [:] )
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include { COOLER_DUMP as COOLER_DUMP_PAIRS} from '../../../../modules/cooler/dump/main.nf' addParams( options: [:] )
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include { COOLER_DUMP as COOLER_DUMP_TABIX} from '../../../../modules/cooler/dump/main.nf' addParams( options: [:] )
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workflow test_cooler_cload_pairix {
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input = [ [ id:'test_pairix', single_end:false ], // meta map
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file(params.test_data['generic']['cooler']['test_pairix_pair_gz'], checkIfExists: true),
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file(params.test_data['generic']['cooler']['test_pairix_pair_gz_px2'], checkIfExists: true)]
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sizes = file(params.test_data['generic']['cooler']['hg19_chrom_sizes'], checkIfExists: true)
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bin_size = 2000000
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COOLER_CLOAD ( input, bin_size, sizes )
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COOLER_DUMP(COOLER_CLOAD.out.cool.map{[it[0], it[2]]}, [])
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}
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workflow test_cooler_cload_pairs {
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input = [ [ id:'test_pairs', single_end:false ], // meta map
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file(params.test_data['generic']['cooler']['test_pairs_pair'], checkIfExists: true),
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[]]
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sizes = file(params.test_data['generic']['cooler']['hg19_chrom_sizes'], checkIfExists: true)
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bin_size = 2000000
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COOLER_CLOAD_PAIRS ( input, bin_size, sizes )
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COOLER_DUMP_PAIRS(COOLER_CLOAD_PAIRS.out.cool.map{[it[0], it[2]]}, [])
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}
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workflow test_cooler_cload_tabix {
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input = [ [ id:'test_tabix', single_end:false ], // meta map
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file(params.test_data['generic']['cooler']['test_tabix_pair_gz'], checkIfExists: true),
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file(params.test_data['generic']['cooler']['test_tabix_pair_gz_tbi'], checkIfExists: true)]
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sizes = file(params.test_data['generic']['cooler']['hg19_chrom_sizes'], checkIfExists: true)
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bin_size = 2000000
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COOLER_CLOAD_TABIX ( input, bin_size, sizes )
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COOLER_DUMP_TABIX(COOLER_CLOAD_TABIX.out.cool.map{[it[0], it[2]]}, [])
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}
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