#!/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'




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 ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
// wget ftp://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("/home/ec2-user/input_files/bams/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam", checkIfExists: true),
//        file("/home/ec2-user/input_files/bams/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai", checkIfExists: true),
//        file("/home/ec2-user/input_files/bams/test2.bam", checkIfExists: true),
//        file("/home/ec2-user/input_files/bams/test2.bam.bai", checkIfExists: true)
//    ]
//
//    ASCAT_PLOIDY_AND_PURITY ( input , "/home/ec2-user/input_files/allele_files/G1000_alleles_hg19_chr", "/home/ec2-user/input_files/loci_files/G1000_alleles_hg19_chr")
//}


// 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("/home/ec2-user/input_files/crams/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram", checkIfExists: true),
//        file("/home/ec2-user/input_files/crams/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai", checkIfExists: true),
//        file("/home/ec2-user/input_files/crams/duplicate_test.cram", checkIfExists: true),
//        file("/home/ec2-user/input_files/crams/duplicate_test.cram.crai", checkIfExists: true)
//    ]
//
//    ASCAT_CRAM ( input , "/home/ec2-user/input_files/allele_files/G1000_alleles_hg19_chr", "/home/ec2-user/input_files/loci_files/G1000_alleles_hg19_chr")
//}