Merge branch 'master' into seqtk/seq-indent-fix
Sateesh Peri
2 years ago
committed by
GitHub
commit
14825510cb
@ -0,0 +1,42 @@
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process BCFTOOLS_ANNOTATE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::bcftools=1.15" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bcftools:1.15--haf5b3da_0':
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'quay.io/biocontainers/bcftools:1.15--haf5b3da_0' }"
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input:
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tuple val(meta), path(input)
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output:
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tuple val(meta), path("*_annotated.vcf.gz"), optional:true , emit: vcf
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tuple val(meta), path("*_annotated.bcf") , optional:true , emit: bcf
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def matcher = input ==~ /\S+\.*vcf\.\S*/
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def output_suffix = matcher ? "vcf.gz" : "bcf"
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def output_type_compressed = matcher ? "z" : "b"
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"""
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bcftools \\
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annotate \\
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$args \\
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--output ${prefix}_annotated.${output_suffix} \\
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--output-type $output_type_compressed \\
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--threads $task.cpus \\
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$input
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' )
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END_VERSIONS
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"""
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}
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@ -0,0 +1,45 @@
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name: bcftools_annotate
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description: Add or remove annotations.
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keywords:
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- bcftools
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- annotate
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- vcf
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- remove
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- add
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tools:
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- annotate:
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description: Add or remove annotations.
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homepage: http://samtools.github.io/bcftools/bcftools.html
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documentation: https://samtools.github.io/bcftools/bcftools.html#annotate
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doi: 10.1093/bioinformatics/btp352
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licence: ['MIT']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- input:
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type: files
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description: Query VCF or BCF file, can be either uncompressed or compressed
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- vcf:
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type: file
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description: Compressed annotated VCF file
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pattern: "*_annotated.vcf.gz"
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- bcf:
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type: file
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description: Compressed annotated BCF file
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pattern: "*_annotated.bcf"
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authors:
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- "@projectoriented"
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@ -0,0 +1,158 @@
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process CONTROLFREEC {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::control-freec=11.6" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
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'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }"
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input:
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tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor)
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path fasta
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path fai
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path snp_position
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path known_snps
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path known_snps_tbi
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path chr_directory
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path mappability
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path target_bed
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path gccontent_profile
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output:
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tuple val(meta), path("*_ratio.BedGraph") , emit: bedgraph, optional: true
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tuple val(meta), path("*_control.cpn") , emit: control_cpn
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tuple val(meta), path("*_sample.cpn") , emit: sample_cpn
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tuple val(meta), path("GC_profile.*.cpn") , emit: gcprofile_cpn, optional:true
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tuple val(meta), path("*_BAF.txt") , emit: BAF
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tuple val(meta), path("*_CNVs") , emit: CNV
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tuple val(meta), path("*_info.txt") , emit: info
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tuple val(meta), path("*_ratio.txt") , emit: ratio
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tuple val(meta), path("config.txt") , emit: config
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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//"General" configurations
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def bedgraphoutput = task.ext.args?["general"]?["bedgraphoutput"] ? "BedGraphOutput = ${task.ext.args["general"]["bedgraphoutput"]}" : ""
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def chr_files = chr_directory ? "chrFiles =\${PWD}/${chr_directory}" : ""
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def chr_length = fai ? "chrLenFile = \${PWD}/${fai}" : ""
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def breakpointthreshold = task.ext.args?["general"]?["breakpointthreshold"] ? "breakPointThreshold = ${task.ext.args["general"]["breakpointthreshold"]}" : ""
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def breakpointtype = task.ext.args?["general"]?["breakpointtype"] ? "breakPointType = ${task.ext.args["general"]["breakpointtype"]}" : ""
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def coefficientofvariation = task.ext.args?["general"]?["coefficient"] ? "coefficientOfVariation = ${task.ext.args["general"]["coefficientofvariation"]}" : ""
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def contamination = task.ext.args?["general"]?["contamination"] ? "contamination = ${task.ext.args["general"]["contamination"]}" : ""
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def contaminationadjustment = task.ext.args?["general"]?["contaminationadjustment"] ? "contaminationAdjustment = ${task.ext.args["general"]["contaminationadjustment"]}" : ""
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def degree = task.ext.args?["general"]?["degree"] ? "degree = ${task.ext.args["general"]["degree"]}" : ""
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def forcegccontentnormalization = task.ext.args?["general"]?["forcegccontentnormalization"] ? "forceGCcontentNormalization = ${task.ext.args["general"]["forcegccontentnormalization"]}" : ""
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def gccontentprofile = gccontent_profile ? "GCcontentProfile = ${gccontent_profile}" : ""
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def mappability = mappability ? "gemMappabilityFile = \${PWD}/${mappability}" : ""
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def intercept = task.ext.args?["general"]?["intercept"] ? "intercept = ${task.ext.args["general"]["intercept"]}" : ""
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def mincnalength = task.ext.args?["general"]?["mincnalength"] ? "minCNAlength = ${task.ext.args["general"]["mincnalength"]}" : ""
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def minmappabilityperwindow = task.ext.args?["general"]?["minmappabilityperwindow"] ? "minMappabilityPerWindow = ${task.ext.args["general"]["minmappabilityperwindow"]}" : ""
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def minexpectedgc = task.ext.args?["general"]?["minexpectedgc"] ? "minExpectedGC = ${task.ext.args["general"]["minexpectedgc"]}" : ""
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def maxexpectedgc = task.ext.args?["general"]?["maxexpectedgc"] ? "maxExpectedGC = ${task.ext.args["general"]["maxexpectedgc"]}" : ""
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def minimalsubclonepresence = task.ext.args?["general"]?["minimalsubclonepresence"] ? "minimalSubclonePresence = ${task.ext.args["general"]["minimalsubclonepresence"]}" : ""
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def noisydata = task.ext.args?["general"]?["noisydata"] ? "noisyData = ${task.ext.args["general"]["noisydata"]}" : ""
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def output = task.ext.prefix ? "outputDir = \${PWD}/${task.ext.prefix}" : ""
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def ploidy = task.ext.args?["general"]?["ploidy"] ? "ploidy = ${task.ext.args["general"]["ploidy"]}" : ""
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def printNA = task.ext.args?["general"]?["printNA"] ? "printNA = ${task.ext.args["general"]["printNA"]}" : ""
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def readcountthreshold = task.ext.args?["general"]?["readcountthreshold"] ? "readCountThreshold = ${task.ext.args["general"]["readcountthreshold"]}" : ""
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def sex = task.ext.args?["general"]?["sex"] ? "sex = ${task.ext.args["general"]["sex"]}" : ""
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def step = task.ext.args?["general"]?["step"] ? "step = ${task.ext.args["general"]["step"]}" : ""
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def telocentromeric = task.ext.args?["general"]?["telocentromeric"] ? "telocentromeric = ${task.ext.args["general"]["telocentromeric"]} " : ""
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def uniquematch = task.ext.args?["general"]?["uniquematch"] ? "uniqueMatch = ${task.ext.args["general"]["uniquematch"]}" : ""
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def window = task.ext.args?["general"]?["window"] ? "window = ${task.ext.args["general"]["window"]}" : ""
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//"Control" configurations
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def matefile_normal = mpileup_normal ? "mateFile = \${PWD}/${mpileup_normal}" : ""
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def matecopynumberfile_normal = cpn_normal ? "mateCopyNumberFile = \${PWD}/${cpn_normal}" : ""
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def minipileup_normal = minipileup_normal ? "miniPileup = \${PWD}/${minipileup_normal}" : ""
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def inputformat_normal = task.ext.args?["control"]?["inputformat"] ? "inputFormat = ${task.ext.args["control"]["inputformat"]}" : ""
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def mateorientation_normal = task.ext.args?["control"]?["mateorientation"] ? "mateOrientation = ${task.ext.args["control"]["mateorientation"]}" : ""
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//"Sample" configuration
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def matefile_tumor = mpileup_tumor ? "mateFile = \${PWD}/${mpileup_tumor}" : ""
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def matecopynumberfile_tumor = cpn_tumor ? "mateCopyNumberFile = \${PWD}/${cpn_tumor}" : ""
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def minipileup_tumor = minipileup_tumor ? "miniPileup = \${PWD}/${minipileup_tumor}" : ""
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def inputformat_tumor = task.ext.args?["sample"]?["inputformat"] ? "inputFormat = ${task.ext.args["sample"]["inputformat"]}" : ""
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def mateorientation_tumor = task.ext.args?["sample"]?["mateorientation"] ? "mateOrientation = ${task.ext.args["sample"]["mateorientation"]}" : ""
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//"BAF" configuration
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def makepileup = snp_position ? "makePileup = \${PWD}/${snp_position}" : ""
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def fastafile = fasta ? "fastaFile = \${PWD}/${fasta}" : ""
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def minimalcoverageperposition = task.ext.args?["BAF"]?["minimalcoverageperposition"] ? "minimalCoveragePerPosition = ${task.ext.args["BAF"]["minimalcoverageperposition"]}" : ""
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def minimalqualityperposition = task.ext.args?["BAF"]?["minimalqualityperposition"] ? "minimalQualityPerPosition = ${task.ext.args["BAF"]["minimalqualityperposition"]}" : ""
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def shiftinquality = task.ext.args?["BAF"]?["shiftinquality"] ? "shiftInQuality = ${task.ext.args["BAF"]["shiftinquality"]}" : ""
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def snpfile = known_snps ? "SNPfile = \$PWD/${known_snps}" : ""
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//"Target" configuration
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def target_bed = target_bed ? "captureRegions = ${target_bed}" : ""
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"""
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touch config.txt
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echo "[general]" >> config.txt
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echo ${bedgraphoutput} >> config.txt
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echo ${breakpointthreshold} >> config.txt
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echo ${breakpointtype} >> config.txt
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echo ${chr_files} >> config.txt
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echo ${chr_length} >> config.txt
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echo ${coefficientofvariation} >> config.txt
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echo ${contamination} >> config.txt
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echo ${contaminationadjustment} >> config.txt
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echo ${degree} >> config.txt
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echo ${forcegccontentnormalization} >> config.txt
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echo ${gccontentprofile} >> config.txt
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echo ${mappability} >> config.txt
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echo ${intercept} >> config.txt
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echo ${mincnalength} >> config.txt
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echo ${minmappabilityperwindow} >> config.txt
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echo ${minexpectedgc} >> config.txt
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echo ${maxexpectedgc} >> config.txt
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echo ${minimalsubclonepresence} >> config.txt
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echo "maxThreads = ${task.cpus}" >> config.txt
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echo ${noisydata} >> config.txt
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echo ${output} >> config.txt
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echo ${ploidy} >> config.txt
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echo ${printNA} >> config.txt
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echo ${readcountthreshold} >> config.txt
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echo ${sex} >> config.txt
|
||||
echo ${step} >> config.txt
|
||||
echo ${telocentromeric} >> config.txt
|
||||
echo ${uniquematch} >> config.txt
|
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echo ${window} >> config.txt
|
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|
||||
echo "[control]" >> config.txt
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echo ${matefile_normal} >> config.txt
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echo ${matecopynumberfile_normal} >> config.txt
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echo ${minipileup_normal} >> config.txt
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echo ${inputformat_normal} >> config.txt
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echo ${mateorientation_normal} >> config.txt
|
||||
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echo "[sample]" >> config.txt
|
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echo ${matefile_tumor} >> config.txt
|
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echo ${matecopynumberfile_tumor} >> config.txt
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echo ${minipileup_tumor} >> config.txt
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||||
echo ${inputformat_tumor} >> config.txt
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echo ${mateorientation_tumor} >> config.txt
|
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|
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echo "[BAF]" >> config.txt
|
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echo ${makepileup} >> config.txt
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echo ${fastafile} >> config.txt
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echo ${minimalcoverageperposition} >> config.txt
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echo ${minimalqualityperposition} >> config.txt
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echo ${shiftinquality} >> config.txt
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echo ${snpfile} >> config.txt
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echo "[target]" >> config.txt
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echo ${target_bed} >> config.txt
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|
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freec -conf config.txt
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||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
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END_VERSIONS
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"""
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}
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@ -0,0 +1,183 @@
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name: controlfreec
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description: Copy number and genotype annotation from whole genome and whole exome sequencing data
|
||||
keywords:
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||||
- cna
|
||||
- cnv
|
||||
- somatic
|
||||
- single
|
||||
- tumor-only
|
||||
tools:
|
||||
- controlfreec:
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||||
description: Copy number and genotype annotation from whole genome and whole exome sequencing data.
|
||||
homepage: http://boevalab.inf.ethz.ch/FREEC
|
||||
documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
|
||||
tool_dev_url: https://github.com/BoevaLab/FREEC/
|
||||
doi: "10.1093/bioinformatics/btq635"
|
||||
licence: ['GPL >=2']
|
||||
|
||||
input:
|
||||
- args:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config.
|
||||
<optional> parameters can be removed from the map, if they are not set. All value must be surrounded by quotes, meta map parameters can be set with, i.e. sex = meta.sex:
|
||||
For default values, please check the documentation above.
|
||||
|
||||
```
|
||||
{
|
||||
[
|
||||
"general" :[
|
||||
"bedgraphoutput": <optional>,
|
||||
"breakpointthreshold": <optional>,
|
||||
"breakpointtype": <optional>,
|
||||
"coefficientofvariation": <optional>,
|
||||
"contamination": <optional>,
|
||||
"contaminationadjustment": <optional>,
|
||||
"degree": <optional>,
|
||||
"forcegccontentnormalization": <optional>,
|
||||
"gccontentprofile": <optional>,
|
||||
"intercept": <optional>,
|
||||
"mincnalength": <optional>,
|
||||
"minmappabilityperwindow": <optional>,
|
||||
"minexpectedgc": <optional>,
|
||||
"maxexpectedgc": <optional>,
|
||||
"minimalsubclonepresence": <optional>,
|
||||
"noisydata": <optional>,
|
||||
"ploidy": <optional>,
|
||||
"printNA": <optional>,
|
||||
"readcountthreshold": <optional >,
|
||||
"sex": <optional>,
|
||||
"step": <optional value>,
|
||||
"telocentromeric": <optional>,
|
||||
"uniquematch": <optional>,
|
||||
"window": <optional>
|
||||
],
|
||||
"control":[
|
||||
"inputformat": <required>,
|
||||
"mateorientation": <optional>,
|
||||
],
|
||||
"sample":[
|
||||
"inputformat": <required>,
|
||||
"mateorientation": <optional>,
|
||||
],
|
||||
"BAF":[
|
||||
"minimalcoverageperposition": <optional>,
|
||||
"minimalqualityperposition": <optional>,
|
||||
"shiftinquality": <optional>
|
||||
]
|
||||
]
|
||||
}
|
||||
```
|
||||
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- mateFile_normal:
|
||||
type: file
|
||||
description: File with mapped reads
|
||||
pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}"
|
||||
- mateFile_tumor:
|
||||
type: file
|
||||
description: File with mapped reads
|
||||
pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}"
|
||||
- cpn_normal:
|
||||
type: file
|
||||
description: Raw copy number profiles (optional)
|
||||
pattern: "*.cpn"
|
||||
- cpn_tumor:
|
||||
type: file
|
||||
description: Raw copy number profiles (optional)
|
||||
pattern: "*.cpn"
|
||||
- minipileup_normal:
|
||||
type: file
|
||||
description: miniPileup file from previous run (optional)
|
||||
pattern: "*.pileup"
|
||||
- minipileup_tumor:
|
||||
type: file
|
||||
description: miniPileup file from previous run (optional)
|
||||
pattern: "*.pileup"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Reference file (optional; required if args 'makePileup' is set)
|
||||
pattern: "*.{fasta,fna,fa}"
|
||||
- fai:
|
||||
type: file
|
||||
description: Fasta index
|
||||
pattern: "*.fai"
|
||||
- snp_position:
|
||||
type: file
|
||||
description:
|
||||
pattern: "*.{}"
|
||||
- known_snps:
|
||||
type: file
|
||||
description: File with known SNPs
|
||||
pattern: "*.{vcf,vcf.gz}"
|
||||
- known_snps_tbi:
|
||||
type: file
|
||||
description: Index of known_snps
|
||||
pattern: "*.tbi"
|
||||
- chr_directory:
|
||||
type: file
|
||||
description: Path to directory with chromosome fasta files (optional, required if gccontentprofile is not provided)
|
||||
pattern: "*/"
|
||||
- mappability:
|
||||
type: file
|
||||
description: Contains information of mappable positions (optional)
|
||||
pattern: "*.gem"
|
||||
- target_bed:
|
||||
type: file
|
||||
description: Sorted bed file containing capture regions (optional)
|
||||
pattern: "*.bed"
|
||||
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- bedgraph:
|
||||
type: file
|
||||
description: Bedgraph format for the UCSC genome browser
|
||||
pattern: ".bedgraph"
|
||||
- control_cpn:
|
||||
type: file
|
||||
description: files with raw copy number profiles
|
||||
pattern: "*_control.cpn"
|
||||
- sample_cpn:
|
||||
type: file
|
||||
description: files with raw copy number profiles
|
||||
pattern: "*_sample.cpn"
|
||||
- gcprofile_cpn:
|
||||
type: file
|
||||
description: file with GC-content profile.
|
||||
pattern: "GC_profile.*.cpn"
|
||||
- BAF:
|
||||
type: file
|
||||
description: file B-allele frequencies for each possibly heterozygous SNP position
|
||||
pattern: "*_BAF.txt"
|
||||
- CNV:
|
||||
type: file
|
||||
description: file with coordinates of predicted copy number alterations.
|
||||
pattern: "*_CNVs"
|
||||
- info:
|
||||
type: file
|
||||
description: parsable file with information about FREEC run
|
||||
pattern: "*_info.txt"
|
||||
- ratio:
|
||||
type: file
|
||||
description: file with ratios and predicted copy number alterations for each window
|
||||
pattern: "*_ratio.txt"
|
||||
- config:
|
||||
type: file
|
||||
description: Config file used to run Control-FREEC
|
||||
pattern: "config.txt"
|
||||
|
||||
authors:
|
||||
- "@FriederikeHanssen"
|
||||
@ -0,0 +1,44 @@
|
||||
process HAMRONIZATION_DEEPARG {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
|
||||
'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(report)
|
||||
val(format)
|
||||
val(software_version)
|
||||
val(reference_db_version)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.json"), optional: true, emit: json
|
||||
tuple val(meta), path("*.tsv") , optional: true, emit: tsv
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
hamronize \\
|
||||
deeparg \\
|
||||
${report} \\
|
||||
$args \\
|
||||
--format ${format} \\
|
||||
--analysis_software_version ${software_version} \\
|
||||
--reference_database_version ${reference_db_version} \\
|
||||
--input_file_name ${prefix} \\
|
||||
> ${prefix}.${format}
|
||||
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,60 @@
|
||||
name: hamronization_deeparg
|
||||
description: Tool to convert and summarize DeepARG outputs using the hAMRonization specification
|
||||
keywords:
|
||||
- amr
|
||||
- antimicrobial resistance
|
||||
- reporting
|
||||
- deeparg
|
||||
tools:
|
||||
- hamronization:
|
||||
description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
|
||||
homepage: https://github.com/pha4ge/hAMRonization/blob/master/README.md
|
||||
documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
|
||||
tool_dev_url: https://github.com/pha4ge/hAMRonization
|
||||
doi: ""
|
||||
licence: ['GNU Lesser General Public v3 (LGPL v3)']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- report:
|
||||
type: file
|
||||
description: Output .mapping.ARG file from DeepARG
|
||||
pattern: "*.mapping.ARG"
|
||||
- format:
|
||||
type: value
|
||||
description: Type of report file to be produced
|
||||
pattern: "tsv|json"
|
||||
- software_version:
|
||||
type: value
|
||||
description: Version of DeepARG used
|
||||
pattern: "[0-9].[0-9].[0-9]"
|
||||
- reference_db_version:
|
||||
type: value
|
||||
description: Database version of DeepARG used
|
||||
pattern: "[0-9]"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- json:
|
||||
type: file
|
||||
description: hAMRonised report in JSON format
|
||||
pattern: "*.json"
|
||||
- tsv:
|
||||
type: file
|
||||
description: hAMRonised report in TSV format
|
||||
pattern: "*.json"
|
||||
|
||||
authors:
|
||||
- "@jfy133"
|
||||
@ -0,0 +1,38 @@
|
||||
process HAMRONIZATION_SUMMARIZE {
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
|
||||
'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
|
||||
|
||||
input:
|
||||
path(reports)
|
||||
val(format)
|
||||
|
||||
output:
|
||||
path("hamronization_combined_report.json"), optional: true, emit: json
|
||||
path("hamronization_combined_report.tsv") , optional: true, emit: tsv
|
||||
path("hamronization_combined_report.html"), optional: true, emit: html
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def outformat = format == 'interactive' ? 'html' : format
|
||||
"""
|
||||
hamronize \\
|
||||
summarize \\
|
||||
${reports.join(' ')} \\
|
||||
-t ${format} \\
|
||||
$args \\
|
||||
-o hamronization_combined_report.${outformat}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,45 @@
|
||||
name: hamronization_summarize
|
||||
description: Tool to summarize and combine all hAMRonization reports into a single file
|
||||
keywords:
|
||||
- amr
|
||||
- antimicrobial resistance
|
||||
- reporting
|
||||
tools:
|
||||
- hamronization:
|
||||
description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
|
||||
homepage: https://github.com/pha4ge/hAMRonization/blob/master/README.md
|
||||
documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
|
||||
tool_dev_url: https://github.com/pha4ge/hAMRonization
|
||||
doi: ""
|
||||
licence: ['GNU Lesser General Public v3 (LGPL v3)']
|
||||
|
||||
input:
|
||||
- reports:
|
||||
type: file
|
||||
description: List of multiple hAMRonization reports in either JSON or TSV format
|
||||
pattern: "*.{json,tsv}"
|
||||
- format:
|
||||
type: value
|
||||
description: Type of final combined report file to be produced
|
||||
pattern: "tsv|json|interactive"
|
||||
|
||||
output:
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- json:
|
||||
type: file
|
||||
description: hAMRonised summary in JSON format
|
||||
pattern: "*.json"
|
||||
- tsv:
|
||||
type: file
|
||||
description: hAMRonised summary in TSV format
|
||||
pattern: "*.json"
|
||||
- html:
|
||||
type: file
|
||||
description: hAMRonised summary in HTML format
|
||||
pattern: "*.html"
|
||||
|
||||
authors:
|
||||
- "@jfy133"
|
||||
@ -0,0 +1,44 @@
|
||||
def VERSION = '1.0.1' // Version information not provided by tool on CLI
|
||||
|
||||
process HPSUISSERO {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/hpsuissero%3A1.0.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/hpsuissero:1.0.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.tsv"), emit: tsv
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def is_compressed = fasta.getName().endsWith(".gz") ? true : false
|
||||
def fasta_name = fasta.getName().replace(".gz", "")
|
||||
"""
|
||||
if [ "$is_compressed" == "true" ]; then
|
||||
gzip -c -d $fasta > $fasta_name
|
||||
fi
|
||||
|
||||
HpsuisSero.sh \\
|
||||
-i $fasta_name \\
|
||||
-o ./ \\
|
||||
-s $prefix \\
|
||||
-x fasta \\
|
||||
-t $task.cpus
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
hpsuissero: $VERSION
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,43 @@
|
||||
name: hpsuissero
|
||||
description: Serotype prediction of Haemophilus parasuis assemblies
|
||||
keywords:
|
||||
- bacteria
|
||||
- fasta
|
||||
- haemophilus
|
||||
tools:
|
||||
- hpsuissero:
|
||||
description: Rapid Haemophilus parasuis serotyping pipeline for Nanpore data
|
||||
homepage: https://github.com/jimmyliu1326/HpsuisSero
|
||||
documentation: https://github.com/jimmyliu1326/HpsuisSero
|
||||
tool_dev_url: https://github.com/jimmyliu1326/HpsuisSero
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Assembly in FASTA format
|
||||
pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- tsv:
|
||||
type: file
|
||||
description: Tab-delimited serotype prediction
|
||||
pattern: "*.{tsv}"
|
||||
|
||||
authors:
|
||||
- "@rpetit3"
|
||||
@ -0,0 +1,35 @@
|
||||
process MAFFT {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::mafft=7.490" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mafft:7.490--h779adbc_0':
|
||||
'quay.io/biocontainers/mafft:7.490--h779adbc_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.fas"), emit: fas
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
mafft \\
|
||||
--thread ${task.cpus} \\
|
||||
${args} \\
|
||||
${fasta} \\
|
||||
> ${prefix}.fas
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
mafft: \$(mafft --version 2>&1 | sed 's/^v//' | sed 's/ (.*)//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,42 @@
|
||||
name: mafft
|
||||
description: Multiple sequence alignment using MAFFT
|
||||
keywords:
|
||||
- msa
|
||||
- multiple sequence alignment
|
||||
tools:
|
||||
- mafft:
|
||||
description: Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
|
||||
homepage: https://mafft.cbrc.jp/alignment/software/
|
||||
documentation: https://mafft.cbrc.jp/alignment/software/manual/manual.html
|
||||
tool_dev_url: https://mafft.cbrc.jp/alignment/software/source.html
|
||||
doi: "10.1093/nar/gkf436"
|
||||
licence: ['BSD']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA file containing the sequences to align
|
||||
pattern: "*.{fa,fasta}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- fas:
|
||||
type: file
|
||||
description: Aligned sequences in FASTA format
|
||||
pattern: "*.{fas}"
|
||||
|
||||
authors:
|
||||
- "@MillironX"
|
||||
@ -0,0 +1,49 @@
|
||||
process PICARD_SORTVCF {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
path reference
|
||||
path sequence_dict
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*_sorted.vcf.gz"), emit: vcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def seq_dict = sequence_dict ? "-SEQUENCE_DICTIONARY $sequence_dict" : ""
|
||||
def reference = reference ? "-REFERENCE_SEQUENCE $reference" : ""
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
} else {
|
||||
avail_mem = task.memory.giga
|
||||
}
|
||||
|
||||
"""
|
||||
picard \\
|
||||
SortVcf \\
|
||||
-Xmx${avail_mem}g \\
|
||||
--INPUT $vcf \\
|
||||
$args \\
|
||||
$seq_dict \\
|
||||
$reference \\
|
||||
--OUTPUT ${prefix}_sorted.vcf.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
picard: \$(picard SortVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,40 @@
|
||||
name: picard_sortvcf
|
||||
description: Sorts vcf files
|
||||
keywords:
|
||||
- sort
|
||||
- vcf
|
||||
tools:
|
||||
- picard:
|
||||
description: Java tools for working with NGS data in the BAM/CRAM/SAM and VCF format
|
||||
homepage: https://broadinstitute.github.io/picard/
|
||||
documentation: https://broadinstitute.github.io/picard/command-line-overview.html#SortVcf
|
||||
licence: ['MIT']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF file
|
||||
pattern: "*.{vcf,vcf.gz}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- vcf:
|
||||
type: file
|
||||
description: Sorted VCF file
|
||||
pattern: "*.{vcf}"
|
||||
|
||||
authors:
|
||||
- "@ramprasadn"
|
||||
@ -0,0 +1,39 @@
|
||||
process PLINK2_SCORE {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' :
|
||||
'quay.io/biocontainers/plink2:2.00a2.3--h712d239_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(pgen), path(psam), path(pvar)
|
||||
path(scorefile)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.sscore"), emit: score
|
||||
path("versions.yml") , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def mem_mb = task.memory.toMega() // plink is greedy
|
||||
"""
|
||||
plink2 \\
|
||||
--threads $task.cpus \\
|
||||
--memory $mem_mb \\
|
||||
--pfile ${pgen.baseName} vzs \\
|
||||
--score ${scorefile} \\
|
||||
$args \\
|
||||
--out ${prefix}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
plink2: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,56 @@
|
||||
name: plink2_score
|
||||
description: Apply a scoring system to each sample in a plink 2 fileset
|
||||
keywords:
|
||||
- plink2
|
||||
- score
|
||||
tools:
|
||||
- plink2:
|
||||
description: |
|
||||
Whole genome association analysis toolset, designed to perform a range
|
||||
of basic, large-scale analyses in a computationally efficient manner
|
||||
homepage: http://www.cog-genomics.org/plink/2.0/
|
||||
documentation: http://www.cog-genomics.org/plink/2.0/general_usage
|
||||
tool_dev_url: None
|
||||
doi: "10.1186/s13742-015-0047-8"
|
||||
licence: ['GPL v3']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- pgen:
|
||||
type: file
|
||||
description: PLINK 2 binary genotype table
|
||||
pattern: "*.{pgen}"
|
||||
- psam:
|
||||
type: file
|
||||
description: PLINK 2 sample information file
|
||||
pattern: "*.{psam}"
|
||||
- pvar:
|
||||
type: file
|
||||
description: PLINK 2 variant information file
|
||||
pattern: "*.{pvar}"
|
||||
- scorefile:
|
||||
type: file
|
||||
description: A text file containing variant identifiers and weights
|
||||
pattern: "*.{scores,txt,scorefile}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- score:
|
||||
type: file
|
||||
description: A text file containing sample scores, in plink 2 .sscore format
|
||||
pattern: "*.{sscore}"
|
||||
|
||||
authors:
|
||||
- "@nebfield"
|
||||
@ -0,0 +1,44 @@
|
||||
def VERSION = '1.0.1' // Version information not provided by tool on CLI
|
||||
|
||||
process SSUISSERO {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::ssuissero=1.0.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/ssuissero%3A1.0.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/ssuissero:1.0.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.tsv"), emit: tsv
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def is_compressed = fasta.getName().endsWith(".gz") ? true : false
|
||||
def fasta_name = fasta.getName().replace(".gz", "")
|
||||
"""
|
||||
if [ "$is_compressed" == "true" ]; then
|
||||
gzip -c -d $fasta > $fasta_name
|
||||
fi
|
||||
|
||||
SsuisSero.sh \\
|
||||
-i $fasta_name \\
|
||||
-o ./ \\
|
||||
-s $prefix \\
|
||||
-x fasta \\
|
||||
-t $task.cpus
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
ssuissero: $VERSION
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,43 @@
|
||||
name: ssuissero
|
||||
description: Serotype prediction of Streptococcus suis assemblies
|
||||
keywords:
|
||||
- bacteria
|
||||
- fasta
|
||||
- streptococcus
|
||||
tools:
|
||||
- ssuissero:
|
||||
description: Rapid Streptococcus suis serotyping pipeline for Nanopore Data
|
||||
homepage: https://github.com/jimmyliu1326/SsuisSero
|
||||
documentation: https://github.com/jimmyliu1326/SsuisSero
|
||||
tool_dev_url: https://github.com/jimmyliu1326/SsuisSero
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Assembly in FASTA format
|
||||
pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- tsv:
|
||||
type: file
|
||||
description: Tab-delimited serotype prediction
|
||||
pattern: "*.{tsv}"
|
||||
|
||||
authors:
|
||||
- "@rpetit3"
|
||||
@ -0,0 +1,33 @@
|
||||
process STRANGER {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::stranger=0.8.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/stranger:0.8.1--pyh5e36f6f_0':
|
||||
'quay.io/biocontainers/stranger:0.8.1--pyh5e36f6f_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.gz"), emit: vcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
stranger \\
|
||||
$args \\
|
||||
$vcf | gzip --no-name > ${prefix}.vcf.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
stranger: \$( stranger --version )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,44 @@
|
||||
name: stranger
|
||||
description: Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.
|
||||
keywords:
|
||||
- STR
|
||||
- repeat_expansions
|
||||
- annotate
|
||||
- vcf
|
||||
tools:
|
||||
- stranger:
|
||||
description: Annotate VCF files with str variants
|
||||
homepage: https://github.com/moonso/stranger
|
||||
documentation: https://github.com/moonso/stranger
|
||||
tool_dev_url: https://github.com/moonso/stranger
|
||||
doi: "10.5281/zenodo.4548873"
|
||||
licence: ['MIT']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF with repeat expansions
|
||||
pattern: "*.{vcf.gz,vcf}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- vcf:
|
||||
type: file
|
||||
description: annotated VCF with keys STR_STATUS, NormalMax and PathologicMin
|
||||
pattern: "*.{vcf.gz}"
|
||||
|
||||
authors:
|
||||
- "@ljmesi"
|
||||
@ -1,31 +1,44 @@
|
||||
- name: adapterremoval test_adapterremoval_single_end
|
||||
command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_single_end -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
|
||||
command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- adapterremoval
|
||||
files:
|
||||
- path: output/adapterremoval/test.discarded.gz
|
||||
- path: output/adapterremoval/test.log
|
||||
md5sum: 2fd3d5d703b63ba33a83021fccf25f77
|
||||
- path: output/adapterremoval/test.trimmed.fastq.gz
|
||||
- path: output/adapterremoval/test.truncated.gz
|
||||
md5sum: 62139afee94defad5b83bdd0b8475a1f
|
||||
- path: output/adapterremoval/versions.yml
|
||||
md5sum: ac5b46719719b7ee62739530b80869fc
|
||||
|
||||
- name: adapterremoval test_adapterremoval_paired_end
|
||||
command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
|
||||
command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- adapterremoval
|
||||
files:
|
||||
- path: output/adapterremoval/test.discarded.gz
|
||||
- path: output/adapterremoval/test.log
|
||||
md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
|
||||
- path: output/adapterremoval/test.pair1.trimmed.fastq.gz
|
||||
- path: output/adapterremoval/test.pair1.truncated.gz
|
||||
md5sum: 294a6277f0139bd597e57c6fa31f39c7
|
||||
- path: output/adapterremoval/test.pair2.trimmed.fastq.gz
|
||||
- path: output/adapterremoval/test.pair2.truncated.gz
|
||||
md5sum: de7b38e2c881bced8671acb1ab452d78
|
||||
- path: output/adapterremoval/test.singleton.truncated.gz
|
||||
- path: output/adapterremoval/versions.yml
|
||||
md5sum: fa621c887897da5a379c719399c17db7
|
||||
|
||||
- name: adapterremoval test_adapterremoval_paired_end_collapse
|
||||
command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
|
||||
command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config
|
||||
tags:
|
||||
- adapterremoval
|
||||
files:
|
||||
- path: output/adapterremoval/test.discarded.gz
|
||||
- path: output/adapterremoval/test.log
|
||||
md5sum: 7f0b2328152226e46101a535cce718b3
|
||||
- path: output/adapterremoval/test.merged.fastq.gz
|
||||
md5sum: 07a8f725bfd3ecbeabdc41b32d898dee
|
||||
md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
|
||||
- path: output/adapterremoval/test.pair1.truncated.gz
|
||||
md5sum: 294a6277f0139bd597e57c6fa31f39c7
|
||||
- path: output/adapterremoval/test.pair2.truncated.gz
|
||||
md5sum: de7b38e2c881bced8671acb1ab452d78
|
||||
- path: output/adapterremoval/test.singleton.truncated.gz
|
||||
- path: output/adapterremoval/versions.yml
|
||||
md5sum: fd428f92a8446e0b34c5ae1c447215b8
|
||||
|
||||
@ -0,0 +1,23 @@
|
||||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { BCFTOOLS_ANNOTATE } from '../../../../modules/bcftools/annotate/main.nf'
|
||||
|
||||
workflow test_bcftools_annotate_out_vcf {
|
||||
|
||||
input = [
|
||||
[ id:'test_compressed_vcf', single_end:false ], // meta map
|
||||
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
|
||||
|
||||
BCFTOOLS_ANNOTATE ( input )
|
||||
}
|
||||
|
||||
workflow test_bcftools_annotate_out_bcf {
|
||||
|
||||
input = [
|
||||
[ id:'test_compressed_bcf', single_end:false ], // meta map
|
||||
file(params.test_data['sarscov2']['illumina']['test_bcf'], checkIfExists: true) ]
|
||||
|
||||
BCFTOOLS_ANNOTATE ( input )
|
||||
}
|
||||
@ -0,0 +1,5 @@
|
||||
process {
|
||||
ext.args = "-x ID,INFO/DP,FORMAT/DP"
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
@ -0,0 +1,19 @@
|
||||
- name: bcftools annotate test_bcftools_annotate_out_vcf
|
||||
command: nextflow run tests/modules/bcftools/annotate -entry test_bcftools_annotate_out_vcf -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bcftools/annotate
|
||||
- bcftools
|
||||
files:
|
||||
- path: output/bcftools/test_compressed_vcf_annotated.vcf.gz
|
||||
- path: output/bcftools/versions.yml
|
||||
md5sum: de86d4d411baef1aaee0e72f519dbe1f
|
||||
|
||||
- name: bcftools annotate test_bcftools_annotate_out_bcf
|
||||
command: nextflow run tests/modules/bcftools/annotate -entry test_bcftools_annotate_out_bcf -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bcftools/annotate
|
||||
- bcftools
|
||||
files:
|
||||
- path: output/bcftools/test_compressed_bcf_annotated.bcf
|
||||
- path: output/bcftools/versions.yml
|
||||
md5sum: a57e62a5a189fe85aabd52c010d88ca6
|
||||
@ -0,0 +1,37 @@
|
||||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { CONTROLFREEC } from '../../../modules/controlfreec/main.nf'
|
||||
include { UNTAR } from '../../../modules/untar/main.nf'
|
||||
workflow test_controlfreec {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false, sex:'XX' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], 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)
|
||||
|
||||
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
|
||||
dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
|
||||
chrfiles = file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true)
|
||||
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
|
||||
|
||||
UNTAR(chrfiles)
|
||||
CONTROLFREEC ( input,
|
||||
fasta,
|
||||
fai,
|
||||
[],
|
||||
dbsnp,
|
||||
dbsnp_tbi,
|
||||
UNTAR.out.untar,
|
||||
[],
|
||||
target_bed,
|
||||
[]
|
||||
)
|
||||
}
|
||||
@ -0,0 +1,26 @@
|
||||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
withName:CONTROLFREEC{
|
||||
ext.args = { [
|
||||
"sample":[
|
||||
inputformat: 'pileup',
|
||||
mateorientation: 'FR'
|
||||
],
|
||||
"general" :[
|
||||
bedgraphoutput: "TRUE",
|
||||
noisydata: "TRUE",
|
||||
minexpectedgc: "0",
|
||||
readcountthreshold: "1",
|
||||
sex: meta.sex,
|
||||
window: "10",
|
||||
],
|
||||
"control":[
|
||||
inputformat: "pileup",
|
||||
mateorientation: "FR"
|
||||
]
|
||||
]
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,22 @@
|
||||
- name: controlfreec test_controlfreec
|
||||
command: nextflow run tests/modules/controlfreec -entry test_controlfreec -c tests/config/nextflow.config
|
||||
tags:
|
||||
- controlfreec
|
||||
files:
|
||||
- path: output/controlfreec/config.txt
|
||||
- path: output/controlfreec/test.mpileup.gz_control.cpn
|
||||
md5sum: 1768b571677c418560e5a8fe203bdc79
|
||||
- path: output/controlfreec/test2.mpileup.gz_BAF.txt
|
||||
md5sum: 3bb7437001cf061a77eaf87b8558c48d
|
||||
- path: output/controlfreec/test2.mpileup.gz_CNVs
|
||||
md5sum: 1f4f5834dbd1490afdb22f6d3091c4c9
|
||||
- path: output/controlfreec/test2.mpileup.gz_info.txt
|
||||
md5sum: 1a3055d35028525ccc9e693cc9f335e0
|
||||
- path: output/controlfreec/test2.mpileup.gz_ratio.BedGraph
|
||||
md5sum: 8ba455b232be20cdcc5bf1e4035e8032
|
||||
- path: output/controlfreec/test2.mpileup.gz_ratio.txt
|
||||
md5sum: b76b2434de710325069e37fb1e132760
|
||||
- path: output/controlfreec/test2.mpileup.gz_sample.cpn
|
||||
md5sum: c80dad58a77b1d7ba6d273999f4b4b4b
|
||||
- path: output/controlfreec/versions.yml
|
||||
md5sum: ff93f6466d4686aab708425782c6c848
|
||||
@ -1,5 +1,6 @@
|
||||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
ext.args = {"--debug" }
|
||||
|
||||
}
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { HAMRONIZATION_DEEPARG } from '../../../../modules/hamronization/deeparg/main.nf'
|
||||
|
||||
workflow test_hamronization_deeparg {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
|
||||
]
|
||||
|
||||
HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2' )
|
||||
}
|
||||
@ -0,0 +1,5 @@
|
||||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
@ -0,0 +1,8 @@
|
||||
- name: hamronization deeparg test_hamronization_deeparg
|
||||
command: nextflow run tests/modules/hamronization/deeparg -entry test_hamronization_deeparg -c tests/config/nextflow.config
|
||||
tags:
|
||||
- hamronization
|
||||
- hamronization/deeparg
|
||||
files:
|
||||
- path: output/hamronization/test.tsv
|
||||
md5sum: 3c315605aca0c5964796bb5fd4cdd522
|
||||
@ -0,0 +1,36 @@
|
||||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { HAMRONIZATION_DEEPARG } from '../../../../modules/hamronization/deeparg/main.nf'
|
||||
include { HAMRONIZATION_DEEPARG as HAMRONIZATION_DEEPARG_SECOND } from '../../../../modules/hamronization/deeparg/main.nf'
|
||||
include { HAMRONIZATION_SUMMARIZE } from '../../../../modules/hamronization/summarize/main.nf'
|
||||
|
||||
workflow test_hamronization_summarize {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
|
||||
]
|
||||
|
||||
input2 = [
|
||||
[ id:'test2', single_end:false ], // meta map
|
||||
file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
|
||||
]
|
||||
|
||||
HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2' )
|
||||
HAMRONIZATION_DEEPARG_SECOND ( input2, 'tsv', '1.0.2', '2' )
|
||||
|
||||
ch_deeparg_run_one = HAMRONIZATION_DEEPARG.out.tsv
|
||||
ch_deeparg_run_two = HAMRONIZATION_DEEPARG_SECOND.out.tsv
|
||||
|
||||
ch_deeparg_run_one
|
||||
.mix( ch_deeparg_run_two )
|
||||
.map{
|
||||
[ it[1] ]
|
||||
}
|
||||
.collect()
|
||||
.set { ch_input_for_summarize }
|
||||
|
||||
HAMRONIZATION_SUMMARIZE ( ch_input_for_summarize , 'json' )
|
||||
}
|
||||
@ -0,0 +1,5 @@
|
||||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
@ -0,0 +1,14 @@
|
||||
- name: hamronization summarize test_hamronization_summarize
|
||||
command: nextflow run tests/modules/hamronization/summarize -entry test_hamronization_summarize -c tests/config/nextflow.config
|
||||
tags:
|
||||
- hamronization
|
||||
- hamronization/summarize
|
||||
files:
|
||||
- path: output/hamronization/hamronization_combined_report.json
|
||||
md5sum: 1623b6cc3b213208a425e023edd94691
|
||||
- path: output/hamronization/test.tsv
|
||||
md5sum: 3c315605aca0c5964796bb5fd4cdd522
|
||||
- path: output/hamronization/test2.tsv
|
||||
md5sum: 453f38502e35261a50a0849dca34f05b
|
||||
- path: output/hamronization/versions.yml
|
||||
md5sum: 99b5046fac643e16ca3362d1baf3284b
|
||||
@ -0,0 +1,15 @@
|
||||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { HPSUISSERO } from '../../../modules/hpsuissero/main.nf'
|
||||
|
||||
workflow test_hpsuissero {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)
|
||||
]
|
||||
|
||||
HPSUISSERO ( input )
|
||||
}
|
||||
@ -0,0 +1,5 @@
|
||||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
@ -0,0 +1,9 @@
|
||||
- name: hpsuissero test_hpsuissero
|
||||
command: nextflow run tests/modules/hpsuissero -entry test_hpsuissero -c tests/config/nextflow.config
|
||||
tags:
|
||||
- hpsuissero
|
||||
files:
|
||||
- path: output/hpsuissero/test_serotyping_res.tsv
|
||||
md5sum: 559dd2ca386eeb58f3975e3204ce9d43
|
||||
- path: output/hpsuissero/versions.yml
|
||||
md5sum: f65438e63a74ac6ee365bfdbbd3f996a
|
||||
@ -0,0 +1,15 @@
|
||||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { MAFFT } from '../../../modules/mafft/main.nf'
|
||||
|
||||
workflow test_mafft {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
|
||||
]
|
||||
|
||||
MAFFT ( input )
|
||||
}
|
||||
@ -0,0 +1,6 @@
|
||||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
ext.args = "--auto"
|
||||
|
||||
}
|
||||
@ -0,0 +1,9 @@
|
||||
- name: mafft test_mafft
|
||||
command: nextflow run tests/modules/mafft -entry test_mafft -c tests/config/nextflow.config
|
||||
tags:
|
||||
- mafft
|
||||
files:
|
||||
- path: output/mafft/test.fas
|
||||
md5sum: 23426611f4a0df532b6708f072bd445b
|
||||
- path: output/mafft/versions.yml
|
||||
md5sum: b1b5ab3728ae17401808335f1c8f8215
|
||||
@ -0,0 +1,18 @@
|
||||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { PICARD_SORTVCF } from '../../../../modules/picard/sortvcf/main.nf'
|
||||
|
||||
workflow test_picard_sortvcf {
|
||||
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
|
||||
]
|
||||
|
||||
fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
|
||||
|
||||
dict = [ file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
|
||||
|
||||
PICARD_SORTVCF ( input, fasta, dict )
|
||||
}
|
||||
@ -0,0 +1,5 @@
|
||||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
@ -0,0 +1,7 @@
|
||||
- name: picard sortvcf
|
||||
command: nextflow run ./tests/modules/picard/sortvcf -entry test_picard_sortvcf -c ./tests/config/nextflow.config -c ./tests/modules/picard/sortvcf/nextflow.config
|
||||
tags:
|
||||
- picard
|
||||
- picard/sortvcf
|
||||
files:
|
||||
- path: output/picard/test_sorted.vcf.gz
|
||||
@ -0,0 +1,24 @@
|
||||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { PLINK2_VCF } from '../../../../modules/plink2/vcf/main.nf'
|
||||
include { PLINK2_SCORE } from '../../../../modules/plink2/score/main.nf'
|
||||
|
||||
workflow test_plink2_score {
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
|
||||
]
|
||||
PLINK2_VCF ( input )
|
||||
|
||||
scorefile = file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_score'], checkIfExists: true)
|
||||
|
||||
PLINK2_VCF.out.pgen
|
||||
.concat(PLINK2_VCF.out.psam, PLINK2_VCF.out.pvar)
|
||||
.groupTuple()
|
||||
.map { it.flatten() }
|
||||
.set { ch_target_genome }
|
||||
|
||||
PLINK2_SCORE ( ch_target_genome, scorefile )
|
||||
}
|
||||
@ -0,0 +1,15 @@
|
||||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
// relabel input variants to a common scheme chr:pos:alt:ref
|
||||
withName: PLINK2_VCF {
|
||||
ext.args = '--set-missing-var-ids @:#:\\$1:\\$2'
|
||||
}
|
||||
|
||||
// scoring really needs an adjustment for small test dataset (n > 50
|
||||
// normally)
|
||||
withName: PLINK2_SCORE {
|
||||
ext.args = 'no-mean-imputation'
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,16 @@
|
||||
- name: plink2 score test_plink2_score
|
||||
command: nextflow run tests/modules/plink2/score -entry test_plink2_score -c tests/config/nextflow.config
|
||||
tags:
|
||||
- plink2
|
||||
- plink2/score
|
||||
files:
|
||||
- path: output/plink2/test.pgen
|
||||
md5sum: fac12ca9041d6950f6b7d60ac2120721
|
||||
- path: output/plink2/test.psam
|
||||
md5sum: e6c714488754cb8448c3dfda08c4c0ea
|
||||
- path: output/plink2/test.pvar.zst
|
||||
md5sum: 98d59e9779a8b62d5032cd98b642a63b
|
||||
- path: output/plink2/test.sscore
|
||||
md5sum: 97bde840f69febd65f2c00e9243126e9
|
||||
- path: output/plink2/versions.yml
|
||||
md5sum: 71499ab14e1583c88ced3a7a4f05bfa7
|
||||
@ -1,12 +1,14 @@
|
||||
- name: plink2 vcf test_plink2_vcf
|
||||
command: nextflow run ./tests/modules/plink2/vcf -entry test_plink2_vcf -c ./tests/config/nextflow.config -c ./tests/modules/plink2/vcf/nextflow.config
|
||||
command: nextflow run tests/modules/plink2/vcf -entry test_plink2_vcf -c tests/config/nextflow.config
|
||||
tags:
|
||||
- plink2/vcf
|
||||
- plink2
|
||||
- plink2/vcf
|
||||
files:
|
||||
- path: output/plink2/test.pgen
|
||||
md5sum: d66d3cd4a6c9cca1a4073d7f4b277041
|
||||
- path: output/plink2/test.psam
|
||||
md5sum: dc3b77d7753a7bed41734323e3549b10
|
||||
- path: output/plink2/test.pvar
|
||||
md5sum: d61e53f847a6335138b584216b4e45d0
|
||||
- path: output/plink2/test.pvar.zst
|
||||
md5sum: b53cccb83e024a39789af5eab8de1c28
|
||||
- path: output/plink2/versions.yml
|
||||
md5sum: 82ada74bc81473b7cba377f696acf54c
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue