mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +00:00
Update intervals (#1278)
* Match target bed to input files * Intervals in getpileupsumamries * more interval updates * change targets in strelka * remove leftover channel * fix checksums * add new test vcfs * add new test vcfs * Update modules/freebayes/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
This commit is contained in:
FriederikeHanssen
GitHub
parent
c8ebd0de36
commit
f5d5926516
21 changed files with 183 additions and 124 deletions
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@ -8,10 +8,9 @@ process FREEBAYES {
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'quay.io/biocontainers/freebayes:1.3.5--py38ha193a2f_3' }"
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input:
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tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index)
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tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index), path(target_bed)
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path fasta
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path fasta_fai
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path targets
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path samples
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path populations
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path cnv
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@ -27,7 +26,7 @@ process FREEBAYES {
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def input = input_2 ? "${input_1} ${input_2}" : "${input_1}"
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def targets_file = targets ? "--target ${targets}" : ""
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def targets_file = target_bed ? "--target ${target_bed}" : ""
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def samples_file = samples ? "--samples ${samples}" : ""
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def populations_file = populations ? "--populations ${populations}" : ""
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def cnv_file = cnv ? "--cnv-map ${cnv}" : ""
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@ -31,7 +31,11 @@ input:
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- input_index:
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type: file
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description: BAM/CRAM/SAM index file
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pattern: "*.bam.bai"
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pattern: "*.{bai,crai}"
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- target_bed:
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type: file
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description: Optional - Limit analysis to targets listed in this BED-format FILE.
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pattern: "*.bed"
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- fasta:
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type: file
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description: reference fasta file
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@ -40,10 +44,6 @@ input:
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type: file
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description: reference fasta file index
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pattern: "*.{fa,fasta}.fai"
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- targets:
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type: file
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description: Optional - Limit analysis to targets listed in this BED-format FILE.
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pattern: "*.bed"
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- samples:
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type: file
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description: Optional - Limit analysis to samples listed (one per line) in the FILE.
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@ -8,10 +8,12 @@ process GATK4_GETPILEUPSUMMARIES {
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'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(bam), path(bai)
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tuple val(meta), path(input), path(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 variants
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path variants_tbi
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path sites
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output:
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tuple val(meta), path('*.pileups.table'), emit: table
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@ -23,9 +25,8 @@ process GATK4_GETPILEUPSUMMARIES {
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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 sitesCommand = ''
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sitesCommand = sites ? " -L ${sites} " : " -L ${variants} "
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def sitesCommand = intervals ? " -L ${intervals} " : " -L ${variants} "
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def reference = fasta ? " -R ${fasta}" :""
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def avail_mem = 3
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if (!task.memory) {
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@ -35,9 +36,10 @@ process GATK4_GETPILEUPSUMMARIES {
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}
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"""
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gatk --java-options "-Xmx${avail_mem}g" GetPileupSummaries \\
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-I $bam \\
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-I $input \\
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-V $variants \\
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$sitesCommand \\
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${reference} \\
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-O ${prefix}.pileups.table \\
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$args
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@ -23,14 +23,30 @@ input:
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- bam:
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- input:
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type: file
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description: BAM file to be summarised.
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pattern: "*.bam"
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- bai:
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description: BAM/CRAM file to be summarised.
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pattern: "*.{bam,cram}"
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- input_index:
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type: file
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description: BAM file index.
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pattern: "*.bam.bai"
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description: BAM/CRAM file index.
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pattern: "*.{bai,crai}"
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- intervals:
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type: file
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description: File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically.
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pattern: "*.interval_list"
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- fasta:
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type: file
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description: The reference fasta file
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pattern: "*.fasta"
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- fai:
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type: file
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description: Index of reference fasta file
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pattern: "*.fasta.fai"
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- dict:
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type: file
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description: GATK sequence dictionary
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pattern: "*.dict"
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- variants:
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type: file
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description: Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified.
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@ -39,10 +55,7 @@ input:
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type: file
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description: Index file for the germline resource.
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pattern: "*.vcf.gz.tbi"
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- sites:
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type: file
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description: File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically.
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pattern: "*.interval_list"
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output:
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- pileup:
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@ -8,11 +8,10 @@ process GATK4_MUTECT2 {
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'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
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input:
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tuple val(meta) , path(input) , path(input_index) , val(which_norm)
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tuple val(meta) , path(input) , path(input_index) , path(intervals), val(which_norm)
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val run_single
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val run_pon
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val run_mito
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val interval_label
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path fasta
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path fai
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path dict
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@ -38,6 +37,7 @@ process GATK4_MUTECT2 {
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def normals_command = ''
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def inputs_command = '-I ' + input.join( ' -I ')
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def interval = intervals ? "-L ${intervals}" : ""
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if(run_pon) {
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panels_command = ''
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@ -48,7 +48,7 @@ process GATK4_MUTECT2 {
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normals_command = ''
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} else if(run_mito){
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panels_command = "-L ${interval_label} --mitochondria-mode"
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panels_command = "-L ${intervals} --mitochondria-mode"
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normals_command = ''
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} else {
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@ -68,6 +68,7 @@ process GATK4_MUTECT2 {
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${inputs_command} \\
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${normals_command} \\
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${panels_command} \\
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${interval} \\
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-O ${prefix}.vcf.gz \\
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$args
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@ -30,6 +30,10 @@ input:
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type: list
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description: list of BAM file indexes, also able to take CRAM indexes as an input
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pattern: "*.{bam.bai/cram.crai}"
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- intervals:
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type: File/string
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description: Specify region the tools is run on.
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pattern: ".{bed,interval_list}/chrM"
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- which_norm:
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type: list
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description: optional list of sample headers contained in the normal sample bam files (these are required for tumor_normal_pair mode)
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@ -46,10 +50,6 @@ input:
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type: boolean
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description: Specify whether or not to run in mitochondria-mode instead of tumor_normal_pair mode
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pattern: "true/false"
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- interval_label:
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type: string
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description: Specify the label used for mitochondrial chromosome when mutect2 is run in mitochondria mode.
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pattern: "chrM"
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- fasta:
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type: file
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description: The reference fasta file
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@ -8,11 +8,9 @@ process STRELKA_GERMLINE {
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'quay.io/biocontainers/strelka:2.9.10--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 (target_bed), path (target_bed_tbi)
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path fasta
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path fai
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path target_bed
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path target_bed_tbi
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output:
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tuple val(meta), path("*variants.vcf.gz") , emit: vcf
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@ -27,7 +25,7 @@ process STRELKA_GERMLINE {
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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 regions = target_bed ? "--exome --callRegions ${target_bed}" : ""
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def regions = target_bed ? "--callRegions ${target_bed}" : ""
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"""
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configureStrelkaGermlineWorkflow.py \\
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--bam $input \\
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@ -8,11 +8,9 @@ process STRELKA_SOMATIC {
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'quay.io/biocontainers/strelka:2.9.10--h9ee0642_1' }"
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input:
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tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi)
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tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi), path(target_bed), path(target_bed_index)
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path fasta
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path fai
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path target_bed
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path target_bed_tbi
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output:
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tuple val(meta), path("*.somatic_indels.vcf.gz") , emit: vcf_indels
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@ -27,15 +25,16 @@ process STRELKA_SOMATIC {
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def options_target_bed = target_bed ? "--exome --callRegions ${target_bed}" : ""
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def options_target_bed = target_bed ? "--callRegions ${target_bed}" : ""
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def options_manta = manta_candidate_small_indels ? "--indelCandidates ${manta_candidate_small_indels}" : ""
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"""
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configureStrelkaSomaticWorkflow.py \\
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--tumor $input_tumor \\
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--normal $input_normal \\
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--referenceFasta $fasta \\
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$options_target_bed \\
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$options_manta \\
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${options_target_bed} \\
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${options_manta} \\
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$args \\
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--runDir strelka
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@ -22,7 +22,7 @@ process TABIX_BGZIPTABIX {
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def args2 = task.ext.args2 ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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bgzip -c $args $input > ${prefix}.gz
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bgzip --threads ${task.cpus} -c $args $input > ${prefix}.gz
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tabix $args2 ${prefix}.gz
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cat <<-END_VERSIONS > versions.yml
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@ -122,6 +122,9 @@ params {
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genome_21_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
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genome_21_dict = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict"
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genome_21_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list"
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genome_21_multi_interval_bed = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
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genome_21_multi_interval_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz"
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genome_21_multi_interval_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi"
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dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
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dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
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@ -262,6 +265,9 @@ params {
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test2_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi"
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test2_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx"
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test_genome21_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
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test_genome21_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"
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test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
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test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
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@ -5,91 +5,98 @@ nextflow.enable.dsl = 2
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include { FREEBAYES } from '../../../modules/freebayes/main.nf'
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workflow test_freebayes {
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targets = []
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input = [ [ id:'test', single_end:false ], // 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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[],
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[]
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[],
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targets
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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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targets = []
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samples = []
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populations = []
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cnv = []
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FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
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FREEBAYES (input, fasta, fai, samples, populations, cnv)
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}
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workflow test_freebayes_bed {
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targets = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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input = [ [ id:'test', single_end:false ], // 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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[],
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[]
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[],
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targets
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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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targets = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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samples = []
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populations = []
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cnv = []
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FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
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FREEBAYES (input, fasta, fai, samples, populations, cnv)
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}
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workflow test_freebayes_cram {
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targets = []
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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_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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[],
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[]
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[],
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targets
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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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targets = []
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samples = []
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populations = []
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cnv = []
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FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
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FREEBAYES (input, fasta, fai, samples, populations, cnv)
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}
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workflow test_freebayes_somatic {
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targets = []
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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_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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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true),
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targets
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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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targets = []
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samples = []
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populations = []
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cnv = []
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FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
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FREEBAYES (input, fasta, fai, samples, populations, cnv)
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}
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workflow test_freebayes_somatic_cram_intervals {
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targets = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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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_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true)
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),
|
||||
targets
|
||||
]
|
||||
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)
|
||||
targets = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||
samples = []
|
||||
populations = []
|
||||
cnv = []
|
||||
|
||||
FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
|
||||
FREEBAYES (input, fasta, fai, samples, populations, cnv)
|
||||
}
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@
|
|||
- freebayes
|
||||
files:
|
||||
- path: output/freebayes/test.vcf.gz
|
||||
md5sum: 81d3e6ce7b6343d088b779567c3803eb
|
||||
md5sum: f28d0b8e2ccedeac0e590ca2ecaac83d
|
||||
- path: output/freebayes/versions.yml
|
||||
md5sum: 53651eb835af65df829241257584a7d2
|
||||
|
||||
|
|
@ -14,7 +14,7 @@
|
|||
- freebayes
|
||||
files:
|
||||
- path: output/freebayes/test.vcf.gz
|
||||
md5sum: 02645d014a63485162a7789007373b2a
|
||||
md5sum: 1927441d1b7a4c48cbb61821de300ad4
|
||||
- path: output/freebayes/versions.yml
|
||||
md5sum: becc93c8a0be580c09d55b955d60a5e1
|
||||
|
||||
|
|
@ -24,7 +24,7 @@
|
|||
- freebayes
|
||||
files:
|
||||
- path: output/freebayes/test.vcf.gz
|
||||
md5sum: 3d0bfcd2129c62f8863952fa4c1054db
|
||||
md5sum: 9b8d1d51d779bbea4086c7f7a2ece641
|
||||
- path: output/freebayes/versions.yml
|
||||
md5sum: 2e5b266edfc6cab81353cfc72c00f67c
|
||||
|
||||
|
|
@ -34,7 +34,7 @@
|
|||
- freebayes
|
||||
files:
|
||||
- path: output/freebayes/test.vcf.gz
|
||||
md5sum: 22fec868210ba3baf685b214bfd8e74b
|
||||
md5sum: dcaa639912174055c1380913d6102c01
|
||||
- path: output/freebayes/versions.yml
|
||||
md5sum: 8fbdb4c052fb3e42b5508a966125fa05
|
||||
|
||||
|
|
@ -44,6 +44,6 @@
|
|||
- freebayes
|
||||
files:
|
||||
- path: output/freebayes/test.vcf.gz
|
||||
md5sum: 527cf2937067bbd4117d95fd472bb928
|
||||
md5sum: b0052a2b83c0ba1b9686d0c96e61712f
|
||||
- path: output/freebayes/versions.yml
|
||||
md5sum: af97e3dfdc086188739907c3460e49e0
|
||||
|
|
|
|||
|
|
@ -8,24 +8,45 @@ workflow test_gatk4_getpileupsummaries_just_variants {
|
|||
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) ,
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ]
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
|
||||
[]
|
||||
]
|
||||
|
||||
variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
|
||||
variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
sites = []
|
||||
|
||||
GATK4_GETPILEUPSUMMARIES ( input , variants , variants_tbi , sites )
|
||||
fasta = []
|
||||
fai = []
|
||||
dict = []
|
||||
GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi )
|
||||
}
|
||||
|
||||
workflow test_gatk4_getpileupsummaries_separate_sites {
|
||||
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) ,
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ]
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) ]
|
||||
|
||||
variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
|
||||
variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
sites = file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true)
|
||||
|
||||
GATK4_GETPILEUPSUMMARIES ( input , variants , variants_tbi , sites )
|
||||
fasta = []
|
||||
fai = []
|
||||
dict = []
|
||||
GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi)
|
||||
}
|
||||
|
||||
workflow test_gatk4_getpileupsummaries_separate_sites_cram {
|
||||
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true) ,
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true)
|
||||
]
|
||||
|
||||
variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
|
||||
variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||||
GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi)
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,17 +1,32 @@
|
|||
- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_just_variants
|
||||
command: nextflow run ./tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_just_variants -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/getpileupsummaries/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_just_variants -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/getpileupsummaries
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.pileups.table
|
||||
md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: dd98374e3b5d35ddd1c6b3fa7e662dc5
|
||||
|
||||
- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites
|
||||
command: nextflow run ./tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/getpileupsummaries/nextflow.config
|
||||
command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/getpileupsummaries
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.pileups.table
|
||||
- path: output/gatk4/test.pileups.table
|
||||
md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 080b6af7df182558aeab117668388d59
|
||||
|
||||
- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites_cram
|
||||
command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites_cram -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4/getpileupsummaries
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.pileups.table
|
||||
md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 33458a9efa6d61c713af9f7b722d7134
|
||||
|
|
|
|||
|
|
@ -12,12 +12,12 @@ workflow test_gatk4_mutect2_tumor_normal_pair {
|
|||
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
|
||||
],
|
||||
[],
|
||||
["normal"]
|
||||
]
|
||||
run_single = false
|
||||
run_pon = false
|
||||
run_mito = false
|
||||
interval_label = []
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||||
|
|
@ -26,19 +26,19 @@ workflow test_gatk4_mutect2_tumor_normal_pair {
|
|||
panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
|
||||
panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
|
||||
GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
|
||||
GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
|
||||
}
|
||||
|
||||
workflow test_gatk4_mutect2_tumor_single {
|
||||
input = [ [ id:'test'], // meta map
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
|
||||
[],
|
||||
[]
|
||||
]
|
||||
run_single = true
|
||||
run_pon = false
|
||||
run_mito = false
|
||||
interval_label = []
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||||
|
|
@ -47,19 +47,19 @@ workflow test_gatk4_mutect2_tumor_single {
|
|||
panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
|
||||
panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
|
||||
GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
|
||||
GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
|
||||
}
|
||||
|
||||
workflow test_gatk4_mutect2_cram_input {
|
||||
input = [ [ id:'test'], // meta map
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)],
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)],
|
||||
[],
|
||||
[]
|
||||
]
|
||||
run_single = true
|
||||
run_pon = false
|
||||
run_mito = false
|
||||
interval_label = []
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||||
|
|
@ -68,19 +68,19 @@ workflow test_gatk4_mutect2_cram_input {
|
|||
panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
|
||||
panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
|
||||
GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
|
||||
GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
|
||||
}
|
||||
|
||||
workflow test_gatk4_mutect2_generate_pon {
|
||||
input = [ [ id:'test'], // meta map
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
|
||||
[],
|
||||
[]
|
||||
]
|
||||
run_single = false
|
||||
run_pon = true
|
||||
run_mito = false
|
||||
interval_label = []
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||||
|
|
@ -89,7 +89,7 @@ workflow test_gatk4_mutect2_generate_pon {
|
|||
panel_of_normals = []
|
||||
panel_of_normals_tbi = []
|
||||
|
||||
GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
|
||||
GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
|
||||
}
|
||||
|
||||
// mitochondria mode would ideally have some mitochondria test data, but since the mitochondria settings only increase detection sensitivity, we can use the chr22 data as a stand in as it is already a small dataset, the extra variants detected compared to generate_pon shows the mode is working.
|
||||
|
|
@ -97,12 +97,12 @@ workflow test_gatk4_mutect2_mitochondria {
|
|||
input = [ [ id:'test'], // meta map
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam'], checkIfExists: true)],
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam_bai'], checkIfExists: true)],
|
||||
[ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)],
|
||||
[]
|
||||
]
|
||||
run_single = false
|
||||
run_pon = false
|
||||
run_mito = true
|
||||
interval_label = 'chr22'
|
||||
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)
|
||||
|
|
@ -111,5 +111,5 @@ workflow test_gatk4_mutect2_mitochondria {
|
|||
panel_of_normals = []
|
||||
panel_of_normals_tbi = []
|
||||
|
||||
GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
|
||||
GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,8 +2,4 @@ process {
|
|||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
withName: GATK4_TEMPFIX_MUTECT2 {
|
||||
ext.args = '--mitochondria-mode'
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -9,28 +9,29 @@ workflow test_strelka_germline {
|
|||
[ id:'test'], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_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)
|
||||
target_bed = []
|
||||
target_bed_tbi = []
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
|
||||
STRELKA_GERMLINE ( input, fasta, fai, target_bed, target_bed_tbi )
|
||||
STRELKA_GERMLINE ( input, fasta, fai)
|
||||
}
|
||||
|
||||
workflow test_strelka_germline_target_bed {
|
||||
|
||||
input = [
|
||||
[ id:'test'], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], 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)
|
||||
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
|
||||
target_bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
|
||||
STRELKA_GERMLINE ( input, fasta, fai, target_bed, target_bed_tbi )
|
||||
STRELKA_GERMLINE ( input, fasta, fai)
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -1,5 +1,7 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
withName: STRELKA_GERMLINE {
|
||||
ext.args = '--exome'
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -12,18 +12,19 @@ workflow test_strelka_somatic {
|
|||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
|
||||
[],[]
|
||||
[],[],
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], 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)
|
||||
bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
|
||||
bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
|
||||
STRELKA_SOMATIC (input, fasta, fai, bed, bed_tbi )
|
||||
STRELKA_SOMATIC (input, fasta, fai )
|
||||
}
|
||||
|
||||
workflow test_strelka__best_practices_somatic {
|
||||
workflow test_strelka_best_practices_somatic {
|
||||
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
|
|
@ -31,14 +32,14 @@ workflow test_strelka__best_practices_somatic {
|
|||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
|
||||
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_genome21_indels_vcf_gz'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz_tbi'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], 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)
|
||||
bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
|
||||
bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
|
||||
STRELKA_SOMATIC ( input, fasta, fai, bed, bed_tbi )
|
||||
STRELKA_SOMATIC ( input, fasta, fai )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,5 +1,7 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
withName: STRELKA_SOMATIC {
|
||||
ext.args = '--exome'
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -6,20 +6,16 @@
|
|||
files:
|
||||
- path: output/strelka/test.somatic_indels.vcf.gz
|
||||
- path: output/strelka/test.somatic_indels.vcf.gz.tbi
|
||||
md5sum: 4cb176febbc8c26d717a6c6e67b9c905
|
||||
- path: output/strelka/test.somatic_snvs.vcf.gz
|
||||
- path: output/strelka/test.somatic_snvs.vcf.gz.tbi
|
||||
md5sum: 4cb176febbc8c26d717a6c6e67b9c905
|
||||
|
||||
- name: strelka somatic test_strelka__best_practices_somatic
|
||||
command: nextflow run ./tests/modules/strelka/somatic -entry test_strelka__best_practices_somatic -c ./tests/config/nextflow.config -c ./tests/modules/strelka/somatic/nextflow.config
|
||||
- name: strelka somatic test_strelka_best_practices_somatic
|
||||
command: nextflow run ./tests/modules/strelka/somatic -entry test_strelka_best_practices_somatic -c ./tests/config/nextflow.config -c ./tests/modules/strelka/somatic/nextflow.config
|
||||
tags:
|
||||
- strelka
|
||||
- strelka/somatic
|
||||
files:
|
||||
- path: output/strelka/test.somatic_indels.vcf.gz
|
||||
- path: output/strelka/test.somatic_indels.vcf.gz.tbi
|
||||
md5sum: 4cb176febbc8c26d717a6c6e67b9c905
|
||||
- path: output/strelka/test.somatic_snvs.vcf.gz
|
||||
- path: output/strelka/test.somatic_snvs.vcf.gz.tbi
|
||||
md5sum: 4cb176febbc8c26d717a6c6e67b9c905
|
||||
|
|
|
|||
Loading…
Reference in a new issue