mirror of
https://github.com/MillironX/nf-core_modules.git
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c189835b1b
* add drafty controlfreec * get sofatware version * use maps in map * update paths to new and soon-to-be merged test files, add more input docu * Stab at documenting args map * Update syntax * Bit more description * Make the linter happy * tests pass locally * Add outputs & docu * tests are failing locally now :/ but cpn file can also be added * All tests passing, need to update test data again to add folder * Clean up files * Clean up files * Clean up files * Don't know how to get the test to run with the direcotry for now. they pass locally though * Make linter happy * Name process back * Update to use tar folder * fix the checksum
37 lines
1.5 KiB
Text
37 lines
1.5 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { CONTROLFREEC } from '../../../modules/controlfreec/main.nf'
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include { UNTAR } from '../../../modules/untar/main.nf'
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workflow test_controlfreec {
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input = [
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[ id:'test', single_end:false, sex:'XX' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
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[],[],[],[]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
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dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
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dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
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chrfiles = file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true)
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target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
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UNTAR(chrfiles)
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CONTROLFREEC ( input,
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fasta,
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fai,
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[],
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dbsnp,
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dbsnp_tbi,
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UNTAR.out.untar,
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[],
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target_bed,
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[]
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)
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}
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