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fix: reduce number of required input files for damage profiler (#612)
* Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
This commit is contained in:
James A. Fellows Yates
GitHub
parent
4e9e732b76
commit
97fe899f79
5 changed files with 144 additions and 35 deletions
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@ -22,25 +22,30 @@ process DAMAGEPROFILER {
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tuple val(meta), path(bam)
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tuple val(meta), path(bam)
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path fasta
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path fasta
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path fai
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path fai
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path specieslist
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output:
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output:
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tuple val(meta), path("${prefix}"), emit: results
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tuple val(meta), path("${prefix}"), emit: results
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path "versions.yml" , emit: versions
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path "versions.yml" , emit: versions
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script:
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script:
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def software = getSoftwareName(task.process)
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def reference = fasta ? "-r $fasta" : ""
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def species_list = specieslist ? "-sf $specieslist" : ""
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"""
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"""
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damageprofiler \\
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damageprofiler \\
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-i $bam \\
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-i $bam \\
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-r $fasta \\
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-o $prefix/ \\
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-o $prefix/ \\
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$options.args \\
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$options.args
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$reference \\
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$species_list
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cat <<-END_VERSIONS > versions.yml
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(damageprofiler -v | sed 's/^DamageProfiler v//')
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${getSoftwareName(task.process)}: \$(damageprofiler -v | sed 's/^DamageProfiler v//')
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END_VERSIONS
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END_VERSIONS
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"""
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"""
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}
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}
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@ -32,12 +32,16 @@ input:
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pattern: "*.{bam,cram,sam}"
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pattern: "*.{bam,cram,sam}"
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- fasta:
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- fasta:
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type: file
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type: file
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description: FASTA reference file
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description: OPTIONAL FASTA reference file
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pattern: "*.{fasta,fna,fa}"
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pattern: "*.{fasta,fna,fa}"
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- fai:
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- fai:
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type: file
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type: file
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description: FASTA index file from samtools faidx
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description: OPTIONAL FASTA index file from samtools faidx
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pattern: "*.{fai}"
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pattern: "*.{fai}"
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- specieslist:
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type: file
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description: OPTIONAL text file with list of target reference headers
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pattern: "*.{txt}"
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output:
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output:
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- versions:
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- versions:
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@ -104,6 +104,7 @@ params {
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genome_gtf = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gtf"
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genome_gtf = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gtf"
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genome_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/genome.sizes"
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genome_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/genome.sizes"
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genome_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed"
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genome_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed"
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genome_header = "${test_data_dir}/genomics/homo_sapiens/genome/genome.header"
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genome_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz"
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genome_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz"
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genome_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz.tbi"
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genome_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz.tbi"
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transcriptome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta"
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transcriptome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta"
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@ -119,18 +120,19 @@ params {
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repeat_expansions = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json"
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repeat_expansions = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json"
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}
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}
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'illumina' {
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'illumina' {
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test_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam"
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test_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam"
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test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai"
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test_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai"
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test_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam"
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test_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam"
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test_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai"
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test_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai"
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test_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam"
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test_paired_end_markduplicates_sorted_referencesn_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.referencesn.txt"
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test_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai"
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test_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam"
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test_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_consensus.bam"
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test_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai"
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test_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_converted.bam"
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test_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_consensus.bam"
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test_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_grouped.bam"
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test_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_converted.bam"
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test_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt"
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test_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_grouped.bam"
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test_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam"
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test_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt"
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test_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam"
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test_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam"
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test_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam"
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test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
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test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
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test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
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test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
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@ -6,10 +6,34 @@ include { DAMAGEPROFILER } from '../../../modules/damageprofiler/main.nf' addPar
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workflow test_damageprofiler {
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workflow test_damageprofiler {
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input = [ [ id:'test', single_end:false ], // meta map
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input = [ [ 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_markduplicates_sorted_bam'], checkIfExists: true) ] ]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fasta = []
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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fai = []
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species_list = []
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DAMAGEPROFILER ( input, fasta, fai )
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DAMAGEPROFILER ( input, fasta, fai, species_list )
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}
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workflow test_damageprofiler_reference {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true) ] ]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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species_list = []
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DAMAGEPROFILER ( input, fasta, fai, species_list )
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}
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workflow test_damageprofiler_specieslist {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true) ] ]
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fasta = []
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fai = []
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species_list = file(params.test_data['homo_sapiens']['genome']['genome_header'], checkIfExists: true)
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DAMAGEPROFILER ( input, fasta, fai, species_list )
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}
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}
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@ -4,13 +4,13 @@
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- damageprofiler
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- damageprofiler
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files:
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files:
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- path: output/damageprofiler/test/3p_freq_misincorporations.txt
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- path: output/damageprofiler/test/3p_freq_misincorporations.txt
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md5sum: da4cac90c78899a7cb6d72d415392b49
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md5sum: de3b84d946a6b63cdcfadf82bf6854c0
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- path: output/damageprofiler/test/3pGtoA_freq.txt
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- path: output/damageprofiler/test/3pGtoA_freq.txt
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md5sum: 8dab75d51a4b943b501d0995169c767f
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md5sum: 61c903b1504ed7d7182570dfc75e4498
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- path: output/damageprofiler/test/5pCtoT_freq.txt
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- path: output/damageprofiler/test/5pCtoT_freq.txt
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md5sum: fcc48ee5f72edff930d627c8bfdd8a5b
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md5sum: 15a75b60ee519b61ce04a83fe3afe855
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- path: output/damageprofiler/test/5p_freq_misincorporations.txt
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- path: output/damageprofiler/test/5p_freq_misincorporations.txt
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md5sum: 54665474f5ef17dcc268567e5eaa7d86
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md5sum: 3b3240d6c1a3491e461b39199a9fcfe3
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- path: output/damageprofiler/test/DamagePlot_five_prime.svg
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- path: output/damageprofiler/test/DamagePlot_five_prime.svg
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- path: output/damageprofiler/test/DamagePlot.pdf
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- path: output/damageprofiler/test/DamagePlot.pdf
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- path: output/damageprofiler/test/DamagePlot_three_prime.svg
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- path: output/damageprofiler/test/DamagePlot_three_prime.svg
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@ -18,19 +18,93 @@
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contains:
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contains:
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- "FINISHED SUCCESSFULLY"
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- "FINISHED SUCCESSFULLY"
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- path: output/damageprofiler/test/dmgprof.json
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- path: output/damageprofiler/test/dmgprof.json
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md5sum: 98499024c7e937896e481f2d3cfbdd3e
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md5sum: 2e54e712d2ae9e32c4c298e5fd8f60fe
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- path: output/damageprofiler/test/DNA_comp_genome.txt
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- path: output/damageprofiler/test/DNA_comp_genome.txt
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md5sum: f91e70760d91a1193a27e360aaddf2fd
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md5sum: fea48af1ecf491b439d36d4a919473df
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- path: output/damageprofiler/test/DNA_composition_sample.txt
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- path: output/damageprofiler/test/DNA_composition_sample.txt
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md5sum: 1257eb3eb42484647bfba2151f9ef04f
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md5sum: 9e17a0b1e5ad4eb13201cd24ad8507dd
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- path: output/damageprofiler/test/edit_distance.pdf
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- path: output/damageprofiler/test/edit_distance.pdf
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- path: output/damageprofiler/test/edit_distance.svg
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- path: output/damageprofiler/test/edit_distance.svg
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- path: output/damageprofiler/test/editDistance.txt
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- path: output/damageprofiler/test/editDistance.txt
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md5sum: af2d2f4a99058ec56eae88ec27779e38
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md5sum: 04d14b449a5afa8b5dbff0dfa762356b
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- path: output/damageprofiler/test/Length_plot_combined_data.svg
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- path: output/damageprofiler/test/Length_plot_combined_data.svg
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- path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
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- path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
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- path: output/damageprofiler/test/Length_plot.pdf
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- path: output/damageprofiler/test/Length_plot.pdf
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- path: output/damageprofiler/test/lgdistribution.txt
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- path: output/damageprofiler/test/lgdistribution.txt
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md5sum: c5d029bf3a92b613310ee23f47d94981
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md5sum: df2e19195185ea9ee05e8e84b2948f36
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- path: output/damageprofiler/test/misincorporation.txt
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- path: output/damageprofiler/test/misincorporation.txt
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md5sum: 3aa6dd749010a492d92a815a83c196a8
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md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c
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- name: damageprofiler_reference
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command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_reference -c tests/config/nextflow.config -dump-channels
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tags:
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- damageprofiler
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files:
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- path: output/damageprofiler/test/3p_freq_misincorporations.txt
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md5sum: de3b84d946a6b63cdcfadf82bf6854c0
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- path: output/damageprofiler/test/3pGtoA_freq.txt
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md5sum: 61c903b1504ed7d7182570dfc75e4498
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- path: output/damageprofiler/test/5pCtoT_freq.txt
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md5sum: 15a75b60ee519b61ce04a83fe3afe855
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- path: output/damageprofiler/test/5p_freq_misincorporations.txt
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md5sum: 3b3240d6c1a3491e461b39199a9fcfe3
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- path: output/damageprofiler/test/DamagePlot_five_prime.svg
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- path: output/damageprofiler/test/DamagePlot.pdf
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- path: output/damageprofiler/test/DamagePlot_three_prime.svg
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- path: output/damageprofiler/test/DamageProfiler.log
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contains:
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- "FINISHED SUCCESSFULLY"
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- path: output/damageprofiler/test/dmgprof.json
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md5sum: 2e54e712d2ae9e32c4c298e5fd8f60fe
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- path: output/damageprofiler/test/DNA_comp_genome.txt
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md5sum: fea48af1ecf491b439d36d4a919473df
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- path: output/damageprofiler/test/DNA_composition_sample.txt
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md5sum: 9e17a0b1e5ad4eb13201cd24ad8507dd
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- path: output/damageprofiler/test/edit_distance.pdf
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- path: output/damageprofiler/test/edit_distance.svg
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- path: output/damageprofiler/test/editDistance.txt
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md5sum: 04d14b449a5afa8b5dbff0dfa762356b
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- path: output/damageprofiler/test/Length_plot_combined_data.svg
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- path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
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- path: output/damageprofiler/test/Length_plot.pdf
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- path: output/damageprofiler/test/lgdistribution.txt
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md5sum: df2e19195185ea9ee05e8e84b2948f36
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- path: output/damageprofiler/test/misincorporation.txt
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md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c
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- name: damageprofiler_specieslist
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command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_specieslist -c tests/config/nextflow.config -dump-channels
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tags:
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- damageprofiler
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files:
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- path: output/damageprofiler/test/chr22/3p_freq_misincorporations.txt
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md5sum: de3b84d946a6b63cdcfadf82bf6854c0
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- path: output/damageprofiler/test/chr22/3pGtoA_freq.txt
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md5sum: 61c903b1504ed7d7182570dfc75e4498
|
||||||
|
- path: output/damageprofiler/test/chr22/5pCtoT_freq.txt
|
||||||
|
md5sum: 15a75b60ee519b61ce04a83fe3afe855
|
||||||
|
- path: output/damageprofiler/test/chr22/5p_freq_misincorporations.txt
|
||||||
|
md5sum: 3b3240d6c1a3491e461b39199a9fcfe3
|
||||||
|
- path: output/damageprofiler/test/chr22/DamagePlot_five_prime.svg
|
||||||
|
- path: output/damageprofiler/test/chr22/DamagePlot.pdf
|
||||||
|
- path: output/damageprofiler/test/chr22/DamagePlot_three_prime.svg
|
||||||
|
- path: output/damageprofiler/test/DamageProfiler.log
|
||||||
|
contains:
|
||||||
|
- "FINISHED SUCCESSFULLY"
|
||||||
|
- path: output/damageprofiler/test/chr22/dmgprof.json
|
||||||
|
md5sum: 2e54e712d2ae9e32c4c298e5fd8f60fe
|
||||||
|
- path: output/damageprofiler/test/chr22/DNA_comp_genome.txt
|
||||||
|
md5sum: fea48af1ecf491b439d36d4a919473df
|
||||||
|
- path: output/damageprofiler/test/chr22/DNA_composition_sample.txt
|
||||||
|
md5sum: 9e17a0b1e5ad4eb13201cd24ad8507dd
|
||||||
|
- path: output/damageprofiler/test/chr22/edit_distance.pdf
|
||||||
|
- path: output/damageprofiler/test/chr22/edit_distance.svg
|
||||||
|
- path: output/damageprofiler/test/chr22/editDistance.txt
|
||||||
|
md5sum: 04d14b449a5afa8b5dbff0dfa762356b
|
||||||
|
- path: output/damageprofiler/test/chr22/Length_plot_combined_data.svg
|
||||||
|
- path: output/damageprofiler/test/chr22/Length_plot_forward_reverse_separated.svg
|
||||||
|
- path: output/damageprofiler/test/chr22/Length_plot.pdf
|
||||||
|
- path: output/damageprofiler/test/chr22/lgdistribution.txt
|
||||||
|
md5sum: df2e19195185ea9ee05e8e84b2948f36
|
||||||
|
- path: output/damageprofiler/test/chr22/misincorporation.txt
|
||||||
|
md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c
|
||||||
|
|
|
||||||
Loading…
Reference in a new issue