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https://github.com/MillironX/nf-core_modules.git
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9ae34a01d1
* Fix typo * Add stub runs for testing input without matched normals * Add missing -stub-run * remove empty file checksum tests and change workflow names * test controlfreec naming * fix output file names * fix output file names * fix output file names * fix conda and container path difference for R scripts * update tar version to work with conda * fix version number in docker * try to fix path to script, pretty sure it won't work * try new ways to set path with wildcard * try which * add which but with escape * remove comment
77 lines
3.2 KiB
Text
77 lines
3.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { CONTROLFREEC_ASSESSSIGNIFICANCE } from '../../../../modules/controlfreec/assesssignificance/main.nf'
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include { CONTROLFREEC_FREEC } from '../../../../modules/controlfreec/freec/main.nf'
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include { UNTAR } from '../../../../modules/untar/main.nf'
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workflow test_controlfreec_assesssignificance {
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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_FREEC (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.map{ it[1] },
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[],
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target_bed,
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[]
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)
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sig_in = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio)
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CONTROLFREEC_ASSESSSIGNIFICANCE ( sig_in )
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}
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workflow test_controlfreec_assesssignificance_single {
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input = [
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[ id:'test', single_end:false, sex:'XX' ], // meta map
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[],
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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_FREEC (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.map{ it[1] },
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[],
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target_bed,
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[]
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)
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sig_in = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio)
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CONTROLFREEC_ASSESSSIGNIFICANCE ( sig_in )
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}
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