#!/usr/bin/env nextflow nextflow.enable.dsl = 2 include { ASCAT as ASCAT_SIMPLE } from '../../../modules/ascat/main.nf' include { ASCAT as ASCAT_PLOIDY_AND_PURITY } from '../../../modules/ascat/main.nf' include { ASCAT as ASCAT_CRAM } from '../../../modules/ascat/main.nf' include { UNZIP as UNZIP_ALLELES } from '../../../modules/unzip/main.nf' include { UNZIP as UNZIP_LOCI } from '../../../modules/unzip/main.nf' include { UNZIP as UNZIP_GC } from '../../../modules/unzip/main.nf' include { UNZIP as UNZIP_RT } from '../../../modules/unzip/main.nf' workflow test_ascat { input = [ [ id:'test', single_end:false ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true) ] ASCAT_SIMPLE ( input , [], [], [], [], [], []) } // extended tests running with 1000 genomes data. Data is downloaded as follows: // wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam // wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai // wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00155/alignment/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam // wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00155/alignment/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai // workflow test_ascat_with_ploidy_and_purity { // input = [ [ id:'test', single_end:false ], // meta map // file("/mnt/volume/ascat/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam", checkIfExists: true), // file("/mnt/volume/ascat/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai", checkIfExists: true), // file("/mnt/volume/ascat/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam", checkIfExists: true), // file("/mnt/volume/ascat/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai", checkIfExists: true) // ] // allele_path = file("/mnt/volume/repos/modules/test_ascat2/G1000_alleles_hg19.zip", checkIfExists: true) // allele_files = [[ id: allele_path.BaseName ], allele_path ] // loci_path = file("/mnt/volume/repos/modules/test_ascat2/G1000_loci_hg19.zip", checkIfExists: true) // loci_files = [[ id: loci_path.BaseName ], loci_path ] // gc_path = file("/mnt/volume/repos/modules/test_ascat2/GC_G1000_hg19.zip", checkIfExists: true) // gc_file = [[ id: gc_path.BaseName ], gc_path ] // rt_path = file("/mnt/volume/repos/modules/test_ascat2/RT_G1000_hg19.zip", checkIfExists: true) // rt_file = [[ id: rt_path.BaseName ], rt_path ] // UNZIP_ALLELES(allele_files) // UNZIP_LOCI(loci_files) // UNZIP_GC(gc_file) // ASCAT_PLOIDY_AND_PURITY ( input , // UNZIP_ALLELES.out.unzipped_archive.map{ it[1] }, // UNZIP_LOCI.out.unzipped_archive.map{ it[1] }, // [], // optional bed_file for WES // [], // optional fasta // UNZIP_GC.out.unzipped_archive.map{ it[1] }, // optional GC_correction // []) // optional RT_correction // // } // extended tests running with 1000 genomes data. Data is downloaded as follows: // wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00145/alignment/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai // wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00145/alignment/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram // wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00146/alignment/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai // wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00146/alignment/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram // workflow test_ascat_with_crams { // input = [ // [ id:'test', single_end:false ], // meta map // file("/mnt/volume/ascat/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram", checkIfExists: true), // file("/mnt/volume/ascat/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai", checkIfExists: true), // file("/mnt/volume/ascat/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram", checkIfExists: true), // file("/mnt/volume/ascat/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai", checkIfExists: true) // ] // allele_path = file("/mnt/volume/repos/modules/test_ascat2/G1000_alleles_hg19.zip", checkIfExists: true) // allele_files = [[ id: allele_path.BaseName ], allele_path ] // loci_path = file("/mnt/volume/repos/modules/test_ascat2/G1000_loci_hg19.zip", checkIfExists: true) // loci_files = [[ id: loci_path.BaseName ], loci_path ] // gc_path = file("/mnt/volume/repos/modules/test_ascat2/GC_G1000_hg19.zip", checkIfExists: true) // gc_file = [[ id: gc_path.BaseName ], gc_path ] // rt_path = file("/mnt/volume/repos/modules/test_ascat2/RT_G1000_hg19.zip", checkIfExists: true) // rt_file = [[ id: rt_path.BaseName ], rt_path ] // fasta = file("/mnt/volume/ascat/human_g1k_v37.fasta", checkIfExists: true) // UNZIP_ALLELES(allele_files) // UNZIP_LOCI(loci_files) // UNZIP_GC(gc_file) // UNZIP_RT(rt_file) // ASCAT_CRAM ( input , // UNZIP_ALLELES.out.unzipped_archive.map{ it[1] }, // UNZIP_LOCI.out.unzipped_archive.map{ it[1] }, // [], // fasta, // UNZIP_GC.out.unzipped_archive.map{ it[1] }, // UNZIP_RT.out.unzipped_archive.map{ it[1] }) // }