diff --git a/modules/bcftools/annotate/main.nf b/modules/bcftools/annotate/main.nf new file mode 100644 index 00000000..40e32047 --- /dev/null +++ b/modules/bcftools/annotate/main.nf @@ -0,0 +1,42 @@ +process BCFTOOLS_ANNOTATE { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::bcftools=1.15" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bcftools:1.15--haf5b3da_0': + 'quay.io/biocontainers/bcftools:1.15--haf5b3da_0' }" + + input: + tuple val(meta), path(input) + + output: + tuple val(meta), path("*_annotated.vcf.gz"), optional:true , emit: vcf + tuple val(meta), path("*_annotated.bcf") , optional:true , emit: bcf + 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 matcher = input ==~ /\S+\.*vcf\.\S*/ + def output_suffix = matcher ? "vcf.gz" : "bcf" + def output_type_compressed = matcher ? "z" : "b" + """ + bcftools \\ + annotate \\ + $args \\ + --output ${prefix}_annotated.${output_suffix} \\ + --output-type $output_type_compressed \\ + --threads $task.cpus \\ + $input + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' ) + END_VERSIONS + """ +} diff --git a/modules/bcftools/annotate/meta.yml b/modules/bcftools/annotate/meta.yml new file mode 100644 index 00000000..3ed124d5 --- /dev/null +++ b/modules/bcftools/annotate/meta.yml @@ -0,0 +1,45 @@ +name: bcftools_annotate +description: Add or remove annotations. +keywords: + - bcftools + - annotate + - vcf + - remove + - add +tools: + - annotate: + description: Add or remove annotations. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: https://samtools.github.io/bcftools/bcftools.html#annotate + doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: files + description: Query VCF or BCF file, can be either uncompressed or compressed +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: Compressed annotated VCF file + pattern: "*_annotated.vcf.gz" + - bcf: + type: file + description: Compressed annotated BCF file + pattern: "*_annotated.bcf" +authors: + - "@projectoriented" diff --git a/modules/bwa/mem/main.nf b/modules/bwa/mem/main.nf index 9a91c77f..27ea6f42 100644 --- a/modules/bwa/mem/main.nf +++ b/modules/bwa/mem/main.nf @@ -2,10 +2,10 @@ process BWA_MEM { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null) + conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' : - 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' : + 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }" input: tuple val(meta), path(reads) diff --git a/modules/bwa/sampe/main.nf b/modules/bwa/sampe/main.nf index e781679e..73345d81 100644 --- a/modules/bwa/sampe/main.nf +++ b/modules/bwa/sampe/main.nf @@ -2,10 +2,10 @@ process BWA_SAMPE { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null) + conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' : - 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' : + 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }" input: tuple val(meta), path(reads), path(sai) diff --git a/modules/bwa/samse/main.nf b/modules/bwa/samse/main.nf index ac04c739..2c327d99 100644 --- a/modules/bwa/samse/main.nf +++ b/modules/bwa/samse/main.nf @@ -2,10 +2,10 @@ process BWA_SAMSE { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null) + conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' : - 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' : + 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }" input: tuple val(meta), path(reads), path(sai) diff --git a/modules/bwamem2/mem/main.nf b/modules/bwamem2/mem/main.nf index 56f595ec..21dfb1d6 100644 --- a/modules/bwamem2/mem/main.nf +++ b/modules/bwamem2/mem/main.nf @@ -2,10 +2,10 @@ process BWAMEM2_MEM { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.12" : null) + conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0' : - 'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' : + 'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' }" input: tuple val(meta), path(reads) diff --git a/modules/controlfreec/main.nf b/modules/controlfreec/main.nf new file mode 100644 index 00000000..21084f64 --- /dev/null +++ b/modules/controlfreec/main.nf @@ -0,0 +1,158 @@ +process CONTROLFREEC { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': + 'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }" + + input: + tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor) + path fasta + path fai + path snp_position + path known_snps + path known_snps_tbi + path chr_directory + path mappability + path target_bed + path gccontent_profile + + output: + tuple val(meta), path("*_ratio.BedGraph") , emit: bedgraph, optional: true + tuple val(meta), path("*_control.cpn") , emit: control_cpn + tuple val(meta), path("*_sample.cpn") , emit: sample_cpn + tuple val(meta), path("GC_profile.*.cpn") , emit: gcprofile_cpn, optional:true + tuple val(meta), path("*_BAF.txt") , emit: BAF + tuple val(meta), path("*_CNVs") , emit: CNV + tuple val(meta), path("*_info.txt") , emit: info + tuple val(meta), path("*_ratio.txt") , emit: ratio + tuple val(meta), path("config.txt") , emit: config + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + //"General" configurations + def bedgraphoutput = task.ext.args?["general"]?["bedgraphoutput"] ? "BedGraphOutput = ${task.ext.args["general"]["bedgraphoutput"]}" : "" + def chr_files = chr_directory ? "chrFiles =\${PWD}/${chr_directory}" : "" + def chr_length = fai ? "chrLenFile = \${PWD}/${fai}" : "" + def breakpointthreshold = task.ext.args?["general"]?["breakpointthreshold"] ? "breakPointThreshold = ${task.ext.args["general"]["breakpointthreshold"]}" : "" + def breakpointtype = task.ext.args?["general"]?["breakpointtype"] ? "breakPointType = ${task.ext.args["general"]["breakpointtype"]}" : "" + def coefficientofvariation = task.ext.args?["general"]?["coefficient"] ? "coefficientOfVariation = ${task.ext.args["general"]["coefficientofvariation"]}" : "" + def contamination = task.ext.args?["general"]?["contamination"] ? "contamination = ${task.ext.args["general"]["contamination"]}" : "" + def contaminationadjustment = task.ext.args?["general"]?["contaminationadjustment"] ? "contaminationAdjustment = ${task.ext.args["general"]["contaminationadjustment"]}" : "" + def degree = task.ext.args?["general"]?["degree"] ? "degree = ${task.ext.args["general"]["degree"]}" : "" + def forcegccontentnormalization = task.ext.args?["general"]?["forcegccontentnormalization"] ? "forceGCcontentNormalization = ${task.ext.args["general"]["forcegccontentnormalization"]}" : "" + def gccontentprofile = gccontent_profile ? "GCcontentProfile = ${gccontent_profile}" : "" + def mappability = mappability ? "gemMappabilityFile = \${PWD}/${mappability}" : "" + def intercept = task.ext.args?["general"]?["intercept"] ? "intercept = ${task.ext.args["general"]["intercept"]}" : "" + def mincnalength = task.ext.args?["general"]?["mincnalength"] ? "minCNAlength = ${task.ext.args["general"]["mincnalength"]}" : "" + def minmappabilityperwindow = task.ext.args?["general"]?["minmappabilityperwindow"] ? "minMappabilityPerWindow = ${task.ext.args["general"]["minmappabilityperwindow"]}" : "" + def minexpectedgc = task.ext.args?["general"]?["minexpectedgc"] ? "minExpectedGC = ${task.ext.args["general"]["minexpectedgc"]}" : "" + def maxexpectedgc = task.ext.args?["general"]?["maxexpectedgc"] ? "maxExpectedGC = ${task.ext.args["general"]["maxexpectedgc"]}" : "" + def minimalsubclonepresence = task.ext.args?["general"]?["minimalsubclonepresence"] ? "minimalSubclonePresence = ${task.ext.args["general"]["minimalsubclonepresence"]}" : "" + def noisydata = task.ext.args?["general"]?["noisydata"] ? "noisyData = ${task.ext.args["general"]["noisydata"]}" : "" + def output = task.ext.prefix ? "outputDir = \${PWD}/${task.ext.prefix}" : "" + def ploidy = task.ext.args?["general"]?["ploidy"] ? "ploidy = ${task.ext.args["general"]["ploidy"]}" : "" + def printNA = task.ext.args?["general"]?["printNA"] ? "printNA = ${task.ext.args["general"]["printNA"]}" : "" + def readcountthreshold = task.ext.args?["general"]?["readcountthreshold"] ? "readCountThreshold = ${task.ext.args["general"]["readcountthreshold"]}" : "" + def sex = task.ext.args?["general"]?["sex"] ? "sex = ${task.ext.args["general"]["sex"]}" : "" + def step = task.ext.args?["general"]?["step"] ? "step = ${task.ext.args["general"]["step"]}" : "" + def telocentromeric = task.ext.args?["general"]?["telocentromeric"] ? "telocentromeric = ${task.ext.args["general"]["telocentromeric"]} " : "" + def uniquematch = task.ext.args?["general"]?["uniquematch"] ? "uniqueMatch = ${task.ext.args["general"]["uniquematch"]}" : "" + def window = task.ext.args?["general"]?["window"] ? "window = ${task.ext.args["general"]["window"]}" : "" + + //"Control" configurations + def matefile_normal = mpileup_normal ? "mateFile = \${PWD}/${mpileup_normal}" : "" + def matecopynumberfile_normal = cpn_normal ? "mateCopyNumberFile = \${PWD}/${cpn_normal}" : "" + def minipileup_normal = minipileup_normal ? "miniPileup = \${PWD}/${minipileup_normal}" : "" + def inputformat_normal = task.ext.args?["control"]?["inputformat"] ? "inputFormat = ${task.ext.args["control"]["inputformat"]}" : "" + def mateorientation_normal = task.ext.args?["control"]?["mateorientation"] ? "mateOrientation = ${task.ext.args["control"]["mateorientation"]}" : "" + + //"Sample" configuration + def matefile_tumor = mpileup_tumor ? "mateFile = \${PWD}/${mpileup_tumor}" : "" + def matecopynumberfile_tumor = cpn_tumor ? "mateCopyNumberFile = \${PWD}/${cpn_tumor}" : "" + def minipileup_tumor = minipileup_tumor ? "miniPileup = \${PWD}/${minipileup_tumor}" : "" + def inputformat_tumor = task.ext.args?["sample"]?["inputformat"] ? "inputFormat = ${task.ext.args["sample"]["inputformat"]}" : "" + def mateorientation_tumor = task.ext.args?["sample"]?["mateorientation"] ? "mateOrientation = ${task.ext.args["sample"]["mateorientation"]}" : "" + + //"BAF" configuration + def makepileup = snp_position ? "makePileup = \${PWD}/${snp_position}" : "" + def fastafile = fasta ? "fastaFile = \${PWD}/${fasta}" : "" + def minimalcoverageperposition = task.ext.args?["BAF"]?["minimalcoverageperposition"] ? "minimalCoveragePerPosition = ${task.ext.args["BAF"]["minimalcoverageperposition"]}" : "" + def minimalqualityperposition = task.ext.args?["BAF"]?["minimalqualityperposition"] ? "minimalQualityPerPosition = ${task.ext.args["BAF"]["minimalqualityperposition"]}" : "" + def shiftinquality = task.ext.args?["BAF"]?["shiftinquality"] ? "shiftInQuality = ${task.ext.args["BAF"]["shiftinquality"]}" : "" + def snpfile = known_snps ? "SNPfile = \$PWD/${known_snps}" : "" + + //"Target" configuration + def target_bed = target_bed ? "captureRegions = ${target_bed}" : "" + """ + touch config.txt + + echo "[general]" >> config.txt + echo ${bedgraphoutput} >> config.txt + echo ${breakpointthreshold} >> config.txt + echo ${breakpointtype} >> config.txt + echo ${chr_files} >> config.txt + echo ${chr_length} >> config.txt + echo ${coefficientofvariation} >> config.txt + echo ${contamination} >> config.txt + echo ${contaminationadjustment} >> config.txt + echo ${degree} >> config.txt + echo ${forcegccontentnormalization} >> config.txt + echo ${gccontentprofile} >> config.txt + echo ${mappability} >> config.txt + echo ${intercept} >> config.txt + echo ${mincnalength} >> config.txt + echo ${minmappabilityperwindow} >> config.txt + echo ${minexpectedgc} >> config.txt + echo ${maxexpectedgc} >> config.txt + echo ${minimalsubclonepresence} >> config.txt + echo "maxThreads = ${task.cpus}" >> config.txt + echo ${noisydata} >> config.txt + echo ${output} >> config.txt + echo ${ploidy} >> config.txt + echo ${printNA} >> config.txt + echo ${readcountthreshold} >> config.txt + echo ${sex} >> config.txt + echo ${step} >> config.txt + echo ${telocentromeric} >> config.txt + echo ${uniquematch} >> config.txt + echo ${window} >> config.txt + + echo "[control]" >> config.txt + echo ${matefile_normal} >> config.txt + echo ${matecopynumberfile_normal} >> config.txt + echo ${minipileup_normal} >> config.txt + echo ${inputformat_normal} >> config.txt + echo ${mateorientation_normal} >> config.txt + + echo "[sample]" >> config.txt + echo ${matefile_tumor} >> config.txt + echo ${matecopynumberfile_tumor} >> config.txt + echo ${minipileup_tumor} >> config.txt + echo ${inputformat_tumor} >> config.txt + echo ${mateorientation_tumor} >> config.txt + + echo "[BAF]" >> config.txt + echo ${makepileup} >> config.txt + echo ${fastafile} >> config.txt + echo ${minimalcoverageperposition} >> config.txt + echo ${minimalqualityperposition} >> config.txt + echo ${shiftinquality} >> config.txt + echo ${snpfile} >> config.txt + + echo "[target]" >> config.txt + echo ${target_bed} >> config.txt + + freec -conf config.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" ) + END_VERSIONS + """ +} diff --git a/modules/controlfreec/meta.yml b/modules/controlfreec/meta.yml new file mode 100644 index 00000000..4d1e8674 --- /dev/null +++ b/modules/controlfreec/meta.yml @@ -0,0 +1,183 @@ +name: controlfreec +description: Copy number and genotype annotation from whole genome and whole exome sequencing data +keywords: + - cna + - cnv + - somatic + - single + - tumor-only +tools: + - controlfreec: + 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. + 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": , + "breakpointthreshold": , + "breakpointtype": , + "coefficientofvariation": , + "contamination": , + "contaminationadjustment": , + "degree": , + "forcegccontentnormalization": , + "gccontentprofile": , + "intercept": , + "mincnalength": , + "minmappabilityperwindow": , + "minexpectedgc": , + "maxexpectedgc": , + "minimalsubclonepresence": , + "noisydata": , + "ploidy": , + "printNA": , + "readcountthreshold": , + "sex": , + "step": , + "telocentromeric": , + "uniquematch": , + "window": + ], + "control":[ + "inputformat": , + "mateorientation": , + ], + "sample":[ + "inputformat": , + "mateorientation": , + ], + "BAF":[ + "minimalcoverageperposition": , + "minimalqualityperposition": , + "shiftinquality": + ] + ] + } + ``` + + - 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" diff --git a/modules/custom/getchromsizes/main.nf b/modules/custom/getchromsizes/main.nf index 39da7d34..bbcfa9be 100644 --- a/modules/custom/getchromsizes/main.nf +++ b/modules/custom/getchromsizes/main.nf @@ -2,10 +2,10 @@ process CUSTOM_GETCHROMSIZES { tag "$fasta" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: path fasta diff --git a/modules/hpsuissero/main.nf b/modules/hpsuissero/main.nf new file mode 100644 index 00000000..4b31f91c --- /dev/null +++ b/modules/hpsuissero/main.nf @@ -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: $VERSION + END_VERSIONS + """ +} diff --git a/modules/hpsuissero/meta.yml b/modules/hpsuissero/meta.yml new file mode 100644 index 00000000..2f48c6c3 --- /dev/null +++ b/modules/hpsuissero/meta.yml @@ -0,0 +1,43 @@ +name: hpsuissero +description: Serotype prediction of Haemophilus parasuis assemblies +keywords: + - bacteria + - fasta + - haemophilus +tools: + - hpsuissero: + description: Rapid Haemophilus parasuis serotyping pipeline for Nanpore data + homepage: https://github.com/jimmyliu1326/HpsuisSero + documentation: https://github.com/jimmyliu1326/HpsuisSero + tool_dev_url: https://github.com/jimmyliu1326/HpsuisSero + doi: "" + licence: ['MIT'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Assembly in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - tsv: + type: file + description: Tab-delimited serotype prediction + pattern: "*.{tsv}" + +authors: + - "@rpetit3" diff --git a/modules/leehom/meta.yml b/modules/leehom/meta.yml index 658db227..05a52743 100644 --- a/modules/leehom/meta.yml +++ b/modules/leehom/meta.yml @@ -61,11 +61,11 @@ output: pattern: "*.r1.fail.fq.gz" - unmerged_r2_fq_pass: type: file - description: Passed unmerged R1 FASTQs + description: Passed unmerged R2 FASTQs pattern: "*.r2.fq.gz" - unmerged_r2_fq_pass: type: file - description: Failed unmerged R1 FASTQs + description: Failed unmerged R2 FASTQs pattern: "*.r2.fail.fq.gz" - log: type: file diff --git a/modules/mafft/main.nf b/modules/mafft/main.nf new file mode 100644 index 00000000..99485b61 --- /dev/null +++ b/modules/mafft/main.nf @@ -0,0 +1,35 @@ +process MAFFT { + tag "$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 + """ +} diff --git a/modules/mafft/meta.yml b/modules/mafft/meta.yml new file mode 100644 index 00000000..10c7f0c2 --- /dev/null +++ b/modules/mafft/meta.yml @@ -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" diff --git a/modules/qualimap/bamqccram/main.nf b/modules/qualimap/bamqccram/main.nf index b9a5538d..ab3fd51a 100644 --- a/modules/qualimap/bamqccram/main.nf +++ b/modules/qualimap/bamqccram/main.nf @@ -2,10 +2,10 @@ process QUALIMAP_BAMQCCRAM { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.12" : null) + conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:4bf11d12f2c3eccf1eb585097c0b6fd31c18c418-0' : - 'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:4bf11d12f2c3eccf1eb585097c0b6fd31c18c418-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:9838874d42d4477d5042782ee019cec9854da7d5-0' : + 'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:9838874d42d4477d5042782ee019cec9854da7d5-0' }" input: tuple val(meta), path(cram), path(crai) diff --git a/modules/samtools/ampliconclip/main.nf b/modules/samtools/ampliconclip/main.nf index 69c2ff7b..4e76b1b4 100644 --- a/modules/samtools/ampliconclip/main.nf +++ b/modules/samtools/ampliconclip/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_AMPLICONCLIP { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(bam) diff --git a/modules/samtools/bam2fq/main.nf b/modules/samtools/bam2fq/main.nf index 4b78a46e..8dd64dc0 100644 --- a/modules/samtools/bam2fq/main.nf +++ b/modules/samtools/bam2fq/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_BAM2FQ { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(inputbam) diff --git a/modules/samtools/depth/main.nf b/modules/samtools/depth/main.nf index d68c5adf..4870b2d8 100644 --- a/modules/samtools/depth/main.nf +++ b/modules/samtools/depth/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_DEPTH { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(bam) diff --git a/modules/samtools/faidx/main.nf b/modules/samtools/faidx/main.nf index b83a4952..7732a4ec 100644 --- a/modules/samtools/faidx/main.nf +++ b/modules/samtools/faidx/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_FAIDX { tag "$fasta" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(fasta) diff --git a/modules/samtools/fastq/main.nf b/modules/samtools/fastq/main.nf index 7eb60117..6408d4a4 100644 --- a/modules/samtools/fastq/main.nf +++ b/modules/samtools/fastq/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_FASTQ { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(bam) diff --git a/modules/samtools/fixmate/main.nf b/modules/samtools/fixmate/main.nf index c1a8164b..14c9db9f 100644 --- a/modules/samtools/fixmate/main.nf +++ b/modules/samtools/fixmate/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_FIXMATE { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(bam) diff --git a/modules/samtools/flagstat/main.nf b/modules/samtools/flagstat/main.nf index c267922b..9e3440ac 100644 --- a/modules/samtools/flagstat/main.nf +++ b/modules/samtools/flagstat/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_FLAGSTAT { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/samtools/idxstats/main.nf b/modules/samtools/idxstats/main.nf index 8a057413..7d5cee17 100644 --- a/modules/samtools/idxstats/main.nf +++ b/modules/samtools/idxstats/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_IDXSTATS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/samtools/index/main.nf b/modules/samtools/index/main.nf index dfe0234f..e41cdcc8 100644 --- a/modules/samtools/index/main.nf +++ b/modules/samtools/index/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_INDEX { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(input) diff --git a/modules/samtools/merge/main.nf b/modules/samtools/merge/main.nf index be6fe32e..7b771677 100644 --- a/modules/samtools/merge/main.nf +++ b/modules/samtools/merge/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_MERGE { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(input_files) diff --git a/modules/samtools/mpileup/main.nf b/modules/samtools/mpileup/main.nf index 77afae60..cea40321 100644 --- a/modules/samtools/mpileup/main.nf +++ b/modules/samtools/mpileup/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_MPILEUP { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(bam) diff --git a/modules/samtools/sort/main.nf b/modules/samtools/sort/main.nf index 0f2237cc..0e2de8ba 100644 --- a/modules/samtools/sort/main.nf +++ b/modules/samtools/sort/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_SORT { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(bam) diff --git a/modules/samtools/stats/main.nf b/modules/samtools/stats/main.nf index f6fe3bfe..6efc9d9a 100644 --- a/modules/samtools/stats/main.nf +++ b/modules/samtools/stats/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_STATS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/samtools/view/main.nf b/modules/samtools/view/main.nf index aee21a4e..75aad063 100644 --- a/modules/samtools/view/main.nf +++ b/modules/samtools/view/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_VIEW { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: tuple val(meta), path(input) diff --git a/modules/ssuissero/main.nf b/modules/ssuissero/main.nf new file mode 100644 index 00000000..d1e5744a --- /dev/null +++ b/modules/ssuissero/main.nf @@ -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 + """ +} diff --git a/modules/ssuissero/meta.yml b/modules/ssuissero/meta.yml new file mode 100644 index 00000000..2c0031e6 --- /dev/null +++ b/modules/ssuissero/meta.yml @@ -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" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 5ae30708..f3cbaa33 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -98,6 +98,10 @@ bbmap/index: - modules/bbmap/index/** - tests/modules/bbmap/index/** +bcftools/annotate: + - modules/bcftools/annotate/** + - tests/modules/bcftools/annotate/** + bcftools/concat: - modules/bcftools/concat/** - tests/modules/bcftools/concat/** @@ -352,6 +356,10 @@ cnvkit/batch: - modules/cnvkit/batch/** - tests/modules/cnvkit/batch/** +controlfreec: + - modules/controlfreec/** + - tests/modules/controlfreec/** + cooler/cload: - modules/cooler/cload/** - tests/modules/cooler/cload/** @@ -807,6 +815,10 @@ homer/makeucscfile: - modules/homer/makeucscfile/** - tests/modules/homer/makeucscfile/** +hpsuissero: + - modules/hpsuissero/** + - tests/modules/hpsuissero/** + ichorcna/createpon: - modules/ichorcna/createpon/** - tests/modules/ichorcna/createpon/** @@ -960,6 +972,10 @@ macs2/callpeak: - modules/macs2/callpeak/** - tests/modules/macs2/callpeak/** +mafft: + - modules/mafft/** + - tests/modules/mafft/** + malt/build: - modules/malt/build/** - tests/modules/malt/build_test/** @@ -1533,6 +1549,10 @@ sratools/prefetch: - modules/sratools/prefetch/** - tests/modules/sratools/prefetch/** +ssuissero: + - modules/ssuissero/** + - tests/modules/ssuissero/** + staphopiasccmec: - modules/staphopiasccmec/** - tests/modules/staphopiasccmec/** diff --git a/tests/config/test_data.config b/tests/config/test_data.config index e28b0cb0..a3c26bcc 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -67,6 +67,8 @@ params { test_computematrix_mat_gz = "${test_data_dir}/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz" + test_bcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.bcf" + test_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf" test_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz" test_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi" @@ -121,10 +123,12 @@ params { genome_21_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" genome_21_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" genome_21_dict = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict" + genome_21_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.sizes" genome_21_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list" genome_21_multi_interval_bed = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" genome_21_multi_interval_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz" genome_21_multi_interval_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi" + genome_21_chromosomes_dir = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz" dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" @@ -154,7 +158,7 @@ params { justhusky_ped = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky.ped" justhusky_minimal_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz" justhusky_minimal_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi" - + vcfanno_tar_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno_grch38_module_test.tar.gz" vcfanno_toml = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml" } @@ -270,6 +274,9 @@ params { test_genome21_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz" test_genome21_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi" + test_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz" + test2_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz" + test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak" test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak" diff --git a/tests/modules/bcftools/annotate/main.nf b/tests/modules/bcftools/annotate/main.nf new file mode 100644 index 00000000..0d096ca9 --- /dev/null +++ b/tests/modules/bcftools/annotate/main.nf @@ -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 ) +} diff --git a/tests/modules/bcftools/annotate/nextflow.config b/tests/modules/bcftools/annotate/nextflow.config new file mode 100644 index 00000000..2670da17 --- /dev/null +++ b/tests/modules/bcftools/annotate/nextflow.config @@ -0,0 +1,5 @@ +process { + ext.args = "-x ID,INFO/DP,FORMAT/DP" + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/bcftools/annotate/test.yml b/tests/modules/bcftools/annotate/test.yml new file mode 100644 index 00000000..e8cdcc4b --- /dev/null +++ b/tests/modules/bcftools/annotate/test.yml @@ -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 diff --git a/tests/modules/bwa/sampe/test.yml b/tests/modules/bwa/sampe/test.yml index fb6d7708..bf221ebc 100644 --- a/tests/modules/bwa/sampe/test.yml +++ b/tests/modules/bwa/sampe/test.yml @@ -5,4 +5,4 @@ - bwa/sampe files: - path: output/bwa/test.bam - md5sum: f6ad85d66d44c5d26e692109d2e34100 + md5sum: 01d1d71c88b6de07ed51d1d06e9e970b diff --git a/tests/modules/bwa/samse/test.yml b/tests/modules/bwa/samse/test.yml index 5a2fe1e3..c45f69dc 100644 --- a/tests/modules/bwa/samse/test.yml +++ b/tests/modules/bwa/samse/test.yml @@ -5,4 +5,4 @@ - bwa/samse files: - path: output/bwa/test.bam - md5sum: 27eb91146e45dee65664c18596be4262 + md5sum: ddfa4a8f6b65d44704a2d9528abc7e79 diff --git a/tests/modules/controlfreec/main.nf b/tests/modules/controlfreec/main.nf new file mode 100644 index 00000000..576a845c --- /dev/null +++ b/tests/modules/controlfreec/main.nf @@ -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, + [] + ) +} diff --git a/tests/modules/controlfreec/nextflow.config b/tests/modules/controlfreec/nextflow.config new file mode 100644 index 00000000..5c4250be --- /dev/null +++ b/tests/modules/controlfreec/nextflow.config @@ -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" + ] + ] + } + } +} diff --git a/tests/modules/controlfreec/test.yml b/tests/modules/controlfreec/test.yml new file mode 100644 index 00000000..14c30205 --- /dev/null +++ b/tests/modules/controlfreec/test.yml @@ -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 diff --git a/tests/modules/hpsuissero/main.nf b/tests/modules/hpsuissero/main.nf new file mode 100644 index 00000000..f66fcd93 --- /dev/null +++ b/tests/modules/hpsuissero/main.nf @@ -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 ) +} diff --git a/tests/modules/hpsuissero/nextflow.config b/tests/modules/hpsuissero/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/hpsuissero/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/hpsuissero/test.yml b/tests/modules/hpsuissero/test.yml new file mode 100644 index 00000000..33b26eb2 --- /dev/null +++ b/tests/modules/hpsuissero/test.yml @@ -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 diff --git a/tests/modules/mafft/main.nf b/tests/modules/mafft/main.nf new file mode 100644 index 00000000..7f50b35a --- /dev/null +++ b/tests/modules/mafft/main.nf @@ -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 ) +} diff --git a/tests/modules/mafft/nextflow.config b/tests/modules/mafft/nextflow.config new file mode 100644 index 00000000..46cc926e --- /dev/null +++ b/tests/modules/mafft/nextflow.config @@ -0,0 +1,6 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + ext.args = "--auto" + +} diff --git a/tests/modules/mafft/test.yml b/tests/modules/mafft/test.yml new file mode 100644 index 00000000..cd40caa7 --- /dev/null +++ b/tests/modules/mafft/test.yml @@ -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 diff --git a/tests/modules/samtools/ampliconclip/test.yml b/tests/modules/samtools/ampliconclip/test.yml index e8fd456c..e9947562 100644 --- a/tests/modules/samtools/ampliconclip/test.yml +++ b/tests/modules/samtools/ampliconclip/test.yml @@ -5,7 +5,7 @@ - samtools/ampliconclip files: - path: output/samtools/test.bam - md5sum: 678f9ab04fbe3206f0f96e170fd833e9 + md5sum: 5d0e8bc9e6059ef3a63ee6328a3935c7 - name: samtools ampliconclip no stats with rejects command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config @@ -14,9 +14,9 @@ - samtools/ampliconclip files: - path: output/samtools/test.bam - md5sum: bbf65ea626539d96c8271e17d1fc988b + md5sum: 2c998295d624c59620b7ffdb0cc080e2 - path: output/samtools/test.cliprejects.bam - md5sum: a0bee15aead020d16d0c81bd9667df46 + md5sum: f3ebba8d91ad29cc4d2d00943e6f6bab - name: samtools ampliconclip with stats with rejects command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_with_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config @@ -25,8 +25,8 @@ - samtools/ampliconclip files: - path: output/samtools/test.bam - md5sum: f5a3611ecad34ba2dde77096e1c7dd93 + md5sum: 87882973b425ab27aad6ef18faf11f25 - path: output/samtools/test.cliprejects.bam - md5sum: 90ee7ce908b4bdb89ab41e4410de9012 + md5sum: eb5e186e1a69864dc2e99a290f02ff78 - path: output/samtools/test.clipstats.txt md5sum: fc23355e1743d47f2541f2cb1a7a0cda diff --git a/tests/modules/samtools/bam2fq/test.yml b/tests/modules/samtools/bam2fq/test.yml index feb994fd..213c7a2d 100644 --- a/tests/modules/samtools/bam2fq/test.yml +++ b/tests/modules/samtools/bam2fq/test.yml @@ -14,9 +14,9 @@ - samtools files: - path: output/samtools/test_1.fq.gz - md5sum: 4522edbe158ec4804765794569f67493 + md5sum: 1c84aadcdca10e97be2b5b6ce773f5ed - path: output/samtools/test_2.fq.gz - md5sum: 7e00ef40d5cfe272b67461381019dcc1 + md5sum: e679ec035d3208785e704458d6b68c8c - path: output/samtools/test_other.fq.gz md5sum: 709872fc2910431b1e8b7074bfe38c67 - path: output/samtools/test_singleton.fq.gz diff --git a/tests/modules/samtools/faidx/test.yml b/tests/modules/samtools/faidx/test.yml index dc2184ee..1a49a0d5 100644 --- a/tests/modules/samtools/faidx/test.yml +++ b/tests/modules/samtools/faidx/test.yml @@ -7,4 +7,4 @@ - path: output/samtools/genome.fasta.fai md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5 - path: output/samtools/versions.yml - md5sum: d56671a7c8f8058944d3d536c3058f7f + md5sum: 6a16b2148a0ab43e6d0506056e6a0409 diff --git a/tests/modules/samtools/fastq/test.yml b/tests/modules/samtools/fastq/test.yml index 39da9889..ff39d61a 100644 --- a/tests/modules/samtools/fastq/test.yml +++ b/tests/modules/samtools/fastq/test.yml @@ -5,6 +5,6 @@ - samtools/fastq files: - path: output/samtools/test_2.fastq.gz - md5sum: 3b1c92f33a44a78d82f8360ab4fdfd61 + md5sum: 51e7a469b554de694799bec982fd722e - path: output/samtools/test_1.fastq.gz - md5sum: 5a3f9c69a032c4ffd9071ea31a14e6f9 + md5sum: 6c2d5b467eb94e058300271a542e34e6 diff --git a/tests/modules/samtools/fixmate/test.yml b/tests/modules/samtools/fixmate/test.yml index 8e87e059..59cd6b41 100644 --- a/tests/modules/samtools/fixmate/test.yml +++ b/tests/modules/samtools/fixmate/test.yml @@ -5,4 +5,4 @@ - samtools/fixmate files: - path: output/samtools/test.bam - md5sum: a4092657a4b17170c7702a76cbf192a1 + md5sum: c7f574bb0c469e0ccfecb6b7210e03c5 diff --git a/tests/modules/samtools/index/test.yml b/tests/modules/samtools/index/test.yml index 7184be8f..09684166 100644 --- a/tests/modules/samtools/index/test.yml +++ b/tests/modules/samtools/index/test.yml @@ -23,4 +23,4 @@ - samtools/index files: - path: output/samtools/test.paired_end.sorted.bam.csi - md5sum: 3dd9e3ed959fca075b88bb8dc3cf7dbd + md5sum: 8d63373007553e74d823fc2b9cbcf84d diff --git a/tests/modules/samtools/sort/test.yml b/tests/modules/samtools/sort/test.yml index dfd2eb69..4535dd09 100644 --- a/tests/modules/samtools/sort/test.yml +++ b/tests/modules/samtools/sort/test.yml @@ -5,4 +5,4 @@ - samtools/sort files: - path: output/samtools/test.sorted.bam - md5sum: 4adc495469724a375d5e1a9f3485e38d + md5sum: a73238d6b896a3a946025d6b13fe9525 diff --git a/tests/modules/samtools/stats/test.yml b/tests/modules/samtools/stats/test.yml index d3444f02..44b7ef8c 100644 --- a/tests/modules/samtools/stats/test.yml +++ b/tests/modules/samtools/stats/test.yml @@ -5,7 +5,7 @@ - samtools files: - path: output/samtools/test.paired_end.sorted.bam.stats - md5sum: 09146eeecfcae2a84fb8615c86cd8d64 + md5sum: 6e3ca28b3e98dade14992dd7ea5fc886 - name: samtools stats test_samtools_stats_cram command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config @@ -14,4 +14,4 @@ - samtools files: - path: output/samtools/test.paired_end.recalibrated.sorted.cram.stats - md5sum: ab49e7380714b7033e374ba1114e5e54 + md5sum: 985455b573444c3743510d603ed41f8c diff --git a/tests/modules/ssuissero/main.nf b/tests/modules/ssuissero/main.nf new file mode 100644 index 00000000..aa285133 --- /dev/null +++ b/tests/modules/ssuissero/main.nf @@ -0,0 +1,15 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SSUISSERO } from '../../../modules/ssuissero/main.nf' + +workflow test_ssuissero { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) + ] + + SSUISSERO ( input ) +} diff --git a/tests/modules/ssuissero/nextflow.config b/tests/modules/ssuissero/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/ssuissero/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/ssuissero/test.yml b/tests/modules/ssuissero/test.yml new file mode 100644 index 00000000..ff61b267 --- /dev/null +++ b/tests/modules/ssuissero/test.yml @@ -0,0 +1,9 @@ +- name: ssuissero test_ssuissero + command: nextflow run tests/modules/ssuissero -entry test_ssuissero -c tests/config/nextflow.config + tags: + - ssuissero + files: + - path: output/ssuissero/test_serotyping_res.tsv + md5sum: 559dd2ca386eeb58f3975e3204ce9d43 + - path: output/ssuissero/versions.yml + md5sum: be29b478690b2047e0413ffe01c85e1e