mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
7daba6a13f
* add unzip alleles + loci * fix the partial absolute prefix path * exchanged deprecated function + added metrics * updated meta * tested logRCorrection + cram input * added BED for WES * added outputs + alleleCounter version * test samtools chr operations, fixed cancerit conda * ch formatting, fasta, bed input * comment out local tests * added metrics, bed, ref_fasta * rm print statement * added stub outputs * rm versions.yml * fix linting * rm fictitious md5sums for stub-run * try fixing top-level of stub versions.yml * ordered inputs alphabetically, ref_fasta -> fasta * rm R system command, adjust meta.yml * prettier yml
113 lines
6.2 KiB
Text
113 lines
6.2 KiB
Text
#!/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] })
|
|
|
|
// }
|
|
|
|
|
|
|