nf-core_modules/tests/modules/controlfreec/assesssignificance/main.nf
FriederikeHanssen 9ae34a01d1
Fix Controlfreec: Add stub runs to test single sample input & make conda work with R scripts (#1504)
* 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
2022-04-08 11:43:40 +02:00

77 lines
3.2 KiB
Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { CONTROLFREEC_ASSESSSIGNIFICANCE } from '../../../../modules/controlfreec/assesssignificance/main.nf'
include { CONTROLFREEC_FREEC } from '../../../../modules/controlfreec/freec/main.nf'
include { UNTAR } from '../../../../modules/untar/main.nf'
workflow test_controlfreec_assesssignificance {
input = [
[ id:'test', single_end:false, sex:'XX' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
[],[],[],[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
UNTAR(chrfiles)
CONTROLFREEC_FREEC (input,
fasta,
fai,
[],
dbsnp,
dbsnp_tbi,
UNTAR.out.untar.map{ it[1] },
[],
target_bed,
[]
)
sig_in = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio)
CONTROLFREEC_ASSESSSIGNIFICANCE ( sig_in )
}
workflow test_controlfreec_assesssignificance_single {
input = [
[ id:'test', single_end:false, sex:'XX' ], // meta map
[],
file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
[],[],[],[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
UNTAR(chrfiles)
CONTROLFREEC_FREEC (input,
fasta,
fai,
[],
dbsnp,
dbsnp_tbi,
UNTAR.out.untar.map{ it[1] },
[],
target_bed,
[]
)
sig_in = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio)
CONTROLFREEC_ASSESSSIGNIFICANCE ( sig_in )
}