mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
e080f4c8ac
* fix: remove left-over unnecessary code * Adds support for meta lists for unzip and untar * Fix test inputs * Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple * Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple * Fix MALTEXTRACT/AMPS * Fix further modules * Fix cellranger * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
37 lines
1.6 KiB
Text
37 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { CONTROLFREEC } from '../../../modules/controlfreec/main.nf'
|
|
include { UNTAR } from '../../../modules/untar/main.nf'
|
|
workflow test_controlfreec {
|
|
|
|
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 ( input,
|
|
fasta,
|
|
fai,
|
|
[],
|
|
dbsnp,
|
|
dbsnp_tbi,
|
|
UNTAR.out.untar.map{ it[1] },
|
|
[],
|
|
target_bed,
|
|
[]
|
|
)
|
|
}
|