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https://github.com/MillironX/nf-core_modules.git
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Change intervals to be part of sample specific input (#1189)
* Change intervals to be part of sample specific input * Fix some tests * Update checksum * Update intervals * Update intervals * Try out gavins idea for adding the file * update test line * update test line * update test line * revert contains line
This commit is contained in:
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13 changed files with 89 additions and 77 deletions
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@ -8,20 +8,22 @@ process GATK4_APPLYBQSR {
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'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
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input:
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tuple val(meta), path(input), path(input_index), path(bqsr_table)
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tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
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path fasta
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path fai
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path dict
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path intervals
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output:
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tuple val(meta), path("*.bam"), emit: bam
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.bam"), emit: bam, optional: true
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tuple val(meta), path("*.cram"), emit: cram, optional: true
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def interval = intervals ? "-L ${intervals}" : ""
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def file_type = input.getExtension()
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK ApplyBQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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@ -35,7 +37,7 @@ process GATK4_APPLYBQSR {
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--bqsr-recal-file $bqsr_table \\
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$interval \\
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--tmp-dir . \\
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-O ${prefix}.bam \\
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-O ${prefix}.${file_type} \\
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$args
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cat <<-END_VERSIONS > versions.yml
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@ -31,6 +31,9 @@ input:
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- bqsr_table:
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type: file
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description: Recalibration table from gatk4_baserecalibrator
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- intervals:
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type: file
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description: Bed file with the genomic regions included in the library (optional)
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- fasta:
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type: file
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description: The reference fasta file
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@ -43,9 +46,7 @@ input:
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type: file
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description: GATK sequence dictionary
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pattern: "*.dict"
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- intervalsBed:
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type: file
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description: Bed file with the genomic regions included in the library (optional)
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output:
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- meta:
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@ -8,11 +8,10 @@ process GATK4_BASERECALIBRATOR {
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'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
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input:
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tuple val(meta), path(input), path(input_index)
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tuple val(meta), path(input), path(input_index), path(intervals)
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path fasta
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path fai
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path dict
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path intervalsBed
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path knownSites
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path knownSites_tbi
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@ -23,14 +22,16 @@ process GATK4_BASERECALIBRATOR {
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : ""
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def intervalsCommand = intervals ? "-L ${intervals}" : ""
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def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ')
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK BaseRecalibrator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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gatk --java-options "-Xmx${avail_mem}g" BaseRecalibrator \
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-R $fasta \
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@ -28,6 +28,9 @@ input:
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type: file
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description: BAI/CRAI file from alignment
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pattern: "*.{bai,crai}"
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- intervals:
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type: file
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description: Bed file with the genomic regions included in the library (optional)
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- fasta:
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type: file
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description: The reference fasta file
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@ -40,9 +43,6 @@ input:
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type: file
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description: GATK sequence dictionary
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pattern: "*.dict"
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- intervalsBed:
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type: file
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description: Bed file with the genomic regions included in the library (optional)
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- knownSites:
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type: file
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description: Bed file with the genomic regions included in the library (optional)
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@ -8,13 +8,12 @@ process GATK4_GENOTYPEGVCFS {
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'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
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input:
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tuple val(meta), path(gvcf), path(gvcf_index)
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tuple val(meta), path(gvcf), path(gvcf_index), path(intervals)
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path fasta
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path fasta_index
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path fasta_dict
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path dbsnp
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path dbsnp_index
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path intervals_bed
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output:
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tuple val(meta), path("*.vcf.gz"), emit: vcf
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@ -25,7 +24,7 @@ process GATK4_GENOTYPEGVCFS {
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def dbsnp_options = dbsnp ? "-D ${dbsnp}" : ""
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def interval_options = intervals_bed ? "-L ${intervals_bed}" : ""
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def interval_options = intervals ? "-L ${intervals}" : ""
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def gvcf_options = gvcf.name.endsWith(".vcf") || gvcf.name.endsWith(".vcf.gz") ? "$gvcf" : "gendb://$gvcf"
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def avail_mem = 3
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if (!task.memory) {
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@ -25,6 +25,9 @@ input:
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description: |
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Tuple of gVCF(.gz) file (first) and its index (second) or the path to a GenomicsDB (and empty)
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pattern: ["*.{vcf,vcf.gz}", "*.{idx,tbi}"]
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- intervals:
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type: file
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description: Bed file with the genomic regions included in the library (optional)
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- fasta:
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type: file
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description: Reference fasta file
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@ -45,10 +48,6 @@ input:
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type: tuple of files
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description: dbSNP VCF index file
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pattern: "*.tbi"
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- intervals_bed:
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type: file
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description: An intevals BED file
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pattern: "*.bed"
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output:
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- meta:
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@ -8,13 +8,12 @@ process GATK4_HAPLOTYPECALLER {
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'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
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input:
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tuple val(meta), path(input), path(input_index)
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tuple val(meta), path(input), path(input_index), path(intervals)
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path fasta
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path fai
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path dict
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path dbsnp
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path dbsnp_tbi
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path interval
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output:
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tuple val(meta), path("*.vcf.gz"), emit: vcf
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@ -24,7 +23,7 @@ process GATK4_HAPLOTYPECALLER {
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def interval_option = interval ? "-L ${interval}" : ""
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def interval_option = intervals ? "-L ${intervals}" : ""
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def dbsnp_option = dbsnp ? "-D ${dbsnp}" : ""
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def avail_mem = 3
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if (!task.memory) {
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@ -29,6 +29,9 @@ input:
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type: file
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description: BAI/CRAI file from alignment
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pattern: "*.{bai,crai}"
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- intervals:
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type: file
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description: Bed file with the genomic regions included in the library (optional)
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- fasta:
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type: file
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description: The reference fasta file
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@ -47,9 +50,6 @@ input:
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- dbsnp_tbi:
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type: file
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description: VCF index of dbsnp (optional)
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- interval:
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type: file
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description: Bed file with the genomic regions included in the library (optional)
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output:
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- meta:
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@ -8,39 +8,40 @@ workflow test_gatk4_applybqsr {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
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[]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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GATK4_APPLYBQSR ( input, fasta, fai, dict, [] )
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GATK4_APPLYBQSR ( input, fasta, fai, dict )
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}
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workflow test_gatk4_applybqsr_intervals {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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intervals = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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GATK4_APPLYBQSR ( input, fasta, fai, dict, intervals )
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GATK4_APPLYBQSR ( input, fasta, fai, dict )
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}
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workflow test_gatk4_applybqsr_cram {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
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file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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]
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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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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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intervals = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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GATK4_APPLYBQSR ( input, fasta, fai, dict, intervals )
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GATK4_APPLYBQSR ( input, fasta, fai, dict )
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}
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@ -26,7 +26,7 @@
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- gatk4
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- gatk4/applybqsr
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files:
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- path: output/gatk4/test.bam
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md5sum: a333f80284a89a8daab28d3686a0b365
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- path: output/gatk4/test.cram
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md5sum: b7659b3b2adaabbe73658dc059dbfdf6
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- path: output/gatk4/versions.yml
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md5sum: 57933f27b3a31b05af3f7c248d365396
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@ -7,7 +7,8 @@ include { GATK4_BASERECALIBRATOR } from '../../../../modules/gatk4/baserecalibra
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workflow test_gatk4_baserecalibrator {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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[]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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@ -15,14 +16,14 @@ workflow test_gatk4_baserecalibrator {
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sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
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sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
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GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, [], sites, sites_tbi )
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GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
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}
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workflow test_gatk4_baserecalibrator_cram {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
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[]
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]
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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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@ -30,28 +31,29 @@ workflow test_gatk4_baserecalibrator_cram {
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sites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
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sites_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
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GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, [], sites, sites_tbi )
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GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
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}
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workflow test_gatk4_baserecalibrator_intervals {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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intervals = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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sites = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
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sites_tbi = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
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GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, intervals, sites, sites_tbi )
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GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
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}
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workflow test_gatk4_baserecalibrator_multiple_sites {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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[]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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@ -63,5 +65,5 @@ workflow test_gatk4_baserecalibrator_multiple_sites {
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file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true)
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]
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GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, [], sites, sites_tbi )
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GATK4_BASERECALIBRATOR ( input, fasta, fai, dict, sites, sites_tbi )
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}
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@ -10,13 +10,15 @@ workflow test_gatk4_genotypegvcfs_vcf_input {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true) ]
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true),
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[]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], [] )
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GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [])
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}
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// Basic parameters with compressed VCF input
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@ -24,13 +26,15 @@ workflow test_gatk4_genotypegvcfs_gz_input {
|
|||
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
|
||||
[]
|
||||
]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], [] )
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [])
|
||||
}
|
||||
|
||||
// Basic parameters + optional dbSNP
|
||||
|
@ -38,7 +42,9 @@ workflow test_gatk4_genotypegvcfs_gz_input_dbsnp {
|
|||
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
|
||||
[]
|
||||
]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
|
@ -47,7 +53,7 @@ workflow test_gatk4_genotypegvcfs_gz_input_dbsnp {
|
|||
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
|
||||
dbsnpIndex = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
|
||||
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex, [] )
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex)
|
||||
}
|
||||
|
||||
// Basic parameters + optional intervals
|
||||
|
@ -55,15 +61,14 @@ workflow test_gatk4_genotypegvcfs_gz_input_intervals {
|
|||
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
intervalsBed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], intervalsBed )
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [])
|
||||
}
|
||||
|
||||
// Basic parameters + optional dbSNP + optional intervals
|
||||
|
@ -71,7 +76,9 @@ workflow test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals {
|
|||
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||
]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
|
@ -80,9 +87,7 @@ workflow test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals {
|
|||
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
|
||||
dbsnpIndex = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
|
||||
|
||||
intervalsBed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex, intervalsBed )
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex )
|
||||
}
|
||||
|
||||
// Basic parameters with GenomicsDB input
|
||||
|
@ -97,9 +102,11 @@ workflow test_gatk4_genotypegvcfs_gendb_input {
|
|||
UNTAR ( test_genomicsdb )
|
||||
gendb = UNTAR.out.untar.collect()
|
||||
gendb.add([])
|
||||
gendb.add([])
|
||||
|
||||
input = Channel.of([ id:'test' ]).combine(gendb)
|
||||
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], [] )
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [])
|
||||
}
|
||||
|
||||
// Basic parameters with GenomicsDB + optional dbSNP
|
||||
|
@ -117,9 +124,10 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp {
|
|||
UNTAR ( test_genomicsdb )
|
||||
gendb = UNTAR.out.untar.collect()
|
||||
gendb.add([])
|
||||
gendb.add([])
|
||||
input = Channel.of([ id:'test' ]).combine(gendb)
|
||||
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex, [] )
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex)
|
||||
}
|
||||
|
||||
// Basic parameters with GenomicsDB + optional intervals
|
||||
|
@ -129,16 +137,15 @@ workflow test_gatk4_genotypegvcfs_gendb_input_intervals {
|
|||
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
intervalsBed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||
|
||||
test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
|
||||
|
||||
UNTAR ( test_genomicsdb )
|
||||
gendb = UNTAR.out.untar.collect()
|
||||
gendb.add([])
|
||||
gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
|
||||
input = Channel.of([ id:'test' ]).combine(gendb)
|
||||
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [], intervalsBed )
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, [], [] )
|
||||
}
|
||||
|
||||
// Basic parameters with GenomicsDB + optional dbSNP + optional intervals
|
||||
|
@ -151,14 +158,13 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals {
|
|||
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
|
||||
dbsnpIndex = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
|
||||
|
||||
intervalsBed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||
|
||||
test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
|
||||
|
||||
UNTAR ( test_genomicsdb )
|
||||
gendb = UNTAR.out.untar.collect()
|
||||
gendb.add([])
|
||||
gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
|
||||
input = Channel.of([ id:'test' ]).combine(gendb)
|
||||
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex, intervalsBed )
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fastaIndex, fastaDict, dbsnp, dbsnpIndex )
|
||||
}
|
||||
|
|
|
@ -7,31 +7,34 @@ include { GATK4_HAPLOTYPECALLER } from '../../../../modules/gatk4/haplotypecalle
|
|||
workflow test_gatk4_haplotypecaller {
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
|
||||
[]
|
||||
]
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, [], [], [] )
|
||||
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, [], [])
|
||||
}
|
||||
|
||||
workflow test_gatk4_haplotypecaller_cram {
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
|
||||
[]
|
||||
]
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, [], [], [] )
|
||||
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, [], [])
|
||||
}
|
||||
|
||||
workflow test_gatk4_haplotypecaller_intervals_dbsnp {
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||
]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
@ -39,7 +42,6 @@ workflow test_gatk4_haplotypecaller_intervals_dbsnp {
|
|||
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
sites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
|
||||
sites_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
|
||||
intervals = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||
|
||||
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi, intervals )
|
||||
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
|
||||
}
|
||||
|
|
Loading…
Reference in a new issue