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