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79a9d5e1ea
NGSCheckMate ncm mode, working on bam files and vcf files to check that (human) samples match as expected Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
63 lines
2.4 KiB
Text
63 lines
2.4 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_BAM} from '../../../../modules/ngscheckmate/ncm/main.nf'
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include { NGSCHECKMATE_NCM as NGSCHECKMATE_NCM_VCF} from '../../../../modules/ngscheckmate/ncm/main.nf'
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include { BEDTOOLS_MAKEWINDOWS } from '../../../../modules/bedtools/makewindows/main.nf'
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include { BCFTOOLS_MPILEUP } from '../../../../modules/bcftools/mpileup/main.nf'
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include { BCFTOOLS_MPILEUP as BCFTOOLS_MPILEUP2 } from '../../../../modules/bcftools/mpileup/main.nf'
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workflow test_ngscheckmate_ncm_bam {
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input = [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
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fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
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inputBed = [ [ id:'test'],
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file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
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BEDTOOLS_MAKEWINDOWS(inputBed, true).
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tab.
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map{it[1]}.
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view().
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set{snp_channel}
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NGSCHECKMATE_NCM_BAM(input, snp_channel, fasta)
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}
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workflow test_ngscheckmate_ncm_vcf {
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input1 = [ [ id:'test1' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
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]
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input2 = [ [ id:'test2' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
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]
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fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
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inputBed = [ [ id:'test'],
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file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
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BCFTOOLS_MPILEUP ( input1, fasta, false )
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BCFTOOLS_MPILEUP2 ( input2, fasta, false )
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BCFTOOLS_MPILEUP2.out.vcf.
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combine( BCFTOOLS_MPILEUP.out.vcf ).
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map { [ it[1], it[3] ] }.
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set { vcf_channel }
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BEDTOOLS_MAKEWINDOWS( inputBed, true ).tab.
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map { it[1] }.
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view().
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set { snp_channel }
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NGSCHECKMATE_NCM_VCF(vcf_channel, snp_channel, fasta)
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}
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