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Merge branch 'nf-core:master' into master

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James A. Fellows Yates 2022-03-01 11:40:01 +01:00 committed by GitHub
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42
modules/bcftools/annotate/main.nf Normal file
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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
"""
}

45
modules/bcftools/annotate/meta.yml Normal file
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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"

6
modules/bwa/mem/main.nf
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@ -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)

6
modules/bwa/sampe/main.nf
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@ -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)

6
modules/bwa/samse/main.nf
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@ -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)

6
modules/bwamem2/mem/main.nf
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@ -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)

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modules/controlfreec/main.nf Normal file
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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
"""
}

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modules/controlfreec/meta.yml Normal file
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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.
<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"

6
modules/custom/getchromsizes/main.nf
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@ -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

44
modules/hpsuissero/main.nf Normal file
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@ -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
"""
}

43
modules/hpsuissero/meta.yml Normal file
View file

@ -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"

4
modules/leehom/meta.yml
View file

@ -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

35
modules/mafft/main.nf Normal file
View file

@ -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
"""
}

42
modules/mafft/meta.yml Normal file
View file

@ -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"

6
modules/qualimap/bamqccram/main.nf
View file

@ -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)

6
modules/samtools/ampliconclip/main.nf
View file

@ -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)

6
modules/samtools/bam2fq/main.nf
View file

@ -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)

6
modules/samtools/depth/main.nf
View file

@ -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)

6
modules/samtools/faidx/main.nf
View file

@ -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)

6
modules/samtools/fastq/main.nf
View file

@ -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)

6
modules/samtools/fixmate/main.nf
View file

@ -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)

6
modules/samtools/flagstat/main.nf
View file

@ -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)

6
modules/samtools/idxstats/main.nf
View file

@ -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)

6
modules/samtools/index/main.nf
View file

@ -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)

6
modules/samtools/merge/main.nf
View file

@ -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)

6
modules/samtools/mpileup/main.nf
View file

@ -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)

6
modules/samtools/sort/main.nf
View file

@ -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)

6
modules/samtools/stats/main.nf
View file

@ -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)

6
modules/samtools/view/main.nf
View file

@ -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)

44
modules/ssuissero/main.nf Normal file
View file

@ -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
"""
}

43
modules/ssuissero/meta.yml Normal file
View file

@ -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"

20
tests/config/pytest_modules.yml
View file

@ -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/**

9
tests/config/test_data.config
View file

@ -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"

23
tests/modules/bcftools/annotate/main.nf Normal file
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@ -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 )
}

5
tests/modules/bcftools/annotate/nextflow.config Normal file
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@ -0,0 +1,5 @@
process {
ext.args = "-x ID,INFO/DP,FORMAT/DP"
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

19
tests/modules/bcftools/annotate/test.yml Normal file
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@ -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

2
tests/modules/bwa/sampe/test.yml
View file

@ -5,4 +5,4 @@
- bwa/sampe
files:
- path: output/bwa/test.bam
md5sum: f6ad85d66d44c5d26e692109d2e34100
md5sum: 01d1d71c88b6de07ed51d1d06e9e970b

2
tests/modules/bwa/samse/test.yml
View file

@ -5,4 +5,4 @@
- bwa/samse
files:
- path: output/bwa/test.bam
md5sum: 27eb91146e45dee65664c18596be4262
md5sum: ddfa4a8f6b65d44704a2d9528abc7e79

37
tests/modules/controlfreec/main.nf Normal file
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@ -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,
[]
)
}

26
tests/modules/controlfreec/nextflow.config Normal file
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@ -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"
]
]
}
}
}

22
tests/modules/controlfreec/test.yml Normal file
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@ -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

15
tests/modules/hpsuissero/main.nf Normal file
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@ -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 )
}

5
tests/modules/hpsuissero/nextflow.config Normal file
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@ -0,0 +1,5 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

9
tests/modules/hpsuissero/test.yml Normal file
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@ -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

15
tests/modules/mafft/main.nf Normal file
View file

@ -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 )
}

6
tests/modules/mafft/nextflow.config Normal file
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@ -0,0 +1,6 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
ext.args = "--auto"
}

9
tests/modules/mafft/test.yml Normal file
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@ -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

10
tests/modules/samtools/ampliconclip/test.yml
View file

@ -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

4
tests/modules/samtools/bam2fq/test.yml
View file

@ -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

2
tests/modules/samtools/faidx/test.yml
View file

@ -7,4 +7,4 @@
- path: output/samtools/genome.fasta.fai
md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
- path: output/samtools/versions.yml
md5sum: d56671a7c8f8058944d3d536c3058f7f
md5sum: 6a16b2148a0ab43e6d0506056e6a0409

4
tests/modules/samtools/fastq/test.yml
View file

@ -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

2
tests/modules/samtools/fixmate/test.yml
View file

@ -5,4 +5,4 @@
- samtools/fixmate
files:
- path: output/samtools/test.bam
md5sum: a4092657a4b17170c7702a76cbf192a1
md5sum: c7f574bb0c469e0ccfecb6b7210e03c5

2
tests/modules/samtools/index/test.yml
View file

@ -23,4 +23,4 @@
- samtools/index
files:
- path: output/samtools/test.paired_end.sorted.bam.csi
md5sum: 3dd9e3ed959fca075b88bb8dc3cf7dbd
md5sum: 8d63373007553e74d823fc2b9cbcf84d

2
tests/modules/samtools/sort/test.yml
View file

@ -5,4 +5,4 @@
- samtools/sort
files:
- path: output/samtools/test.sorted.bam
md5sum: 4adc495469724a375d5e1a9f3485e38d
md5sum: a73238d6b896a3a946025d6b13fe9525

4
tests/modules/samtools/stats/test.yml
View file

@ -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

15
tests/modules/ssuissero/main.nf Normal file
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@ -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 )
}

5
tests/modules/ssuissero/nextflow.config Normal file
View file

@ -0,0 +1,5 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

9
tests/modules/ssuissero/test.yml Normal file
View file

@ -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