mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
64 lines
2.4 KiB
Text
64 lines
2.4 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_BAM} from '../../../../modules/ngscheckmate/ncm/main.nf'
|
||
|
|
include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_VCF} from '../../../../modules/ngscheckmate/ncm/main.nf'
|
||
|
|
|
||
|
|
include { BEDTOOLS_MAKEWINDOWS } from '../../../../modules/bedtools/makewindows/main.nf'
|
||
|
|
|
||
|
|
include { BCFTOOLS_MPILEUP } from '../../../../modules/bcftools/mpileup/main.nf'
|
||
|
|
include { BCFTOOLS_MPILEUP as BCFTOOLS_MPILEUP2 } from '../../../../modules/bcftools/mpileup/main.nf'
|
||
|
|
|
||
|
|
workflow test_ngscheckmate_ncm_bam {
|
||
|
|
input = [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
|
||
|
|
|
||
|
|
fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
|
||
|
|
|
||
|
|
inputBed = [ [ id:'test'],
|
||
|
|
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
|
||
|
|
|
||
|
|
BEDTOOLS_MAKEWINDOWS(inputBed, true).
|
||
|
|
tab.
|
||
|
|
map{it[1]}.
|
||
|
|
view().
|
||
|
|
set{snp_channel}
|
||
|
|
|
||
|
|
NGSCHECKMATE_NCM_BAM(input, snp_channel, fasta)
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_ngscheckmate_ncm_vcf {
|
||
|
|
input1 = [ [ id:'test1' ], // meta map
|
||
|
|
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
|
||
|
|
]
|
||
|
|
|
||
|
|
input2 = [ [ id:'test2' ], // meta map
|
||
|
|
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
|
||
|
|
]
|
||
|
|
|
||
|
|
fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
|
||
|
|
|
||
|
|
inputBed = [ [ id:'test'],
|
||
|
|
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
|
||
|
|
|
||
|
|
BCFTOOLS_MPILEUP ( input1, fasta, false )
|
||
|
|
BCFTOOLS_MPILEUP2 ( input2, fasta, false )
|
||
|
|
|
||
|
|
BCFTOOLS_MPILEUP2.out.vcf.
|
||
|
|
combine( BCFTOOLS_MPILEUP.out.vcf ).
|
||
|
|
map { [ it[1], it[3] ] }.
|
||
|
|
set { vcf_channel }
|
||
|
|
|
||
|
|
BEDTOOLS_MAKEWINDOWS( inputBed, true ).tab.
|
||
|
|
map { it[1] }.
|
||
|
|
view().
|
||
|
|
set { snp_channel }
|
||
|
|
|
||
|
|
NGSCHECKMATE_NCM_VCF(vcf_channel, snp_channel, fasta)
|
||
|
|
}
|
||
|
|
|
||
|
|
|