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Merge branch 'master' into sexdeterrmine

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Thiseas C. Lamnidis 2022-06-10 11:03:18 +02:00 committed by GitHub
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1
modules/bamtools/convert/meta.yml
View file

@ -42,7 +42,6 @@ output:
type: file
description: File containing software versions
pattern: "versions.yml"
## TODO nf-core: Delete / customise this example output
- out:
type: file
description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml)

2
modules/bcftools/concat/main.nf
View file

@ -8,7 +8,7 @@ process BCFTOOLS_CONCAT {
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(vcfs)
tuple val(meta), path(vcfs), path(tbi)
output:
tuple val(meta), path("*.gz"), emit: vcf

5
modules/bcftools/concat/meta.yml
View file

@ -25,6 +25,11 @@ input:
description: |
List containing 2 or more vcf files
e.g. [ 'file1.vcf', 'file2.vcf' ]
- tbi:
type: files
description: |
List containing 2 or more index files (optional)
e.g. [ 'file1.tbi', 'file2.tbi' ]
output:
- meta:
type: map

61
modules/bcftools/roh/main.nf Normal file
View file

@ -0,0 +1,61 @@
process BCFTOOLS_ROH {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
input:
tuple val(meta), path(vcf), path(tbi)
tuple path(af_file), path(af_file_tbi)
path genetic_map
path regions_file
path samples_file
path targets_file
output:
tuple val(meta), path("*.roh"), emit: roh
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 af_read = af_file ? "--AF-file ${af_file}" : ''
def gen_map = genetic_map ? "--genetic-map ${genetic_map}" : ''
def reg_file = regions_file ? "--regions-file ${regions_file}" : ''
def samp_file = samples_file ? "--samples-file ${samples_file}" : ''
def targ_file = targets_file ? "--targets-file ${targets_file}" : ''
"""
bcftools \\
roh \\
$args \\
$af_read \\
$gen_map \\
$reg_file \\
$samp_file \\
$targ_file \\
-o ${prefix}.roh \\
$vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.roh
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
}

58
modules/bcftools/roh/meta.yml Normal file
View file

@ -0,0 +1,58 @@
name: "bcftools_roh"
description: A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.
keywords:
- roh
tools:
- "roh":
description: "A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered."
homepage: https://www.htslib.org/
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: VCF file
pattern: "*.{vcf,.vcf.gz}"
- af_file:
type: file
description: "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF."
- af_file_tbi:
type: file
description: "tbi index of af_file."
- genetic_map:
type: file
description: "Genetic map in the format required also by IMPUTE2."
- regions_file:
type: file
description: "Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)."
- samples_file:
type: file
description: "File of sample names to include or exclude if prefixed with '^'."
- targets_file:
type: file
description: "Targets can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)."
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"
- roh:
type: file
description: Contains site-specific and/or per-region runs of homo/autozygosity calls.
pattern: "*.{roh}"
authors:
- "@ramprasadn"

148
modules/cnvkit/batch/main.nf
View file

@ -10,6 +10,7 @@ process CNVKIT_BATCH {
input:
tuple val(meta), path(tumor), path(normal)
path fasta
path fasta_fai
path targets
path reference
@ -28,35 +29,69 @@ process CNVKIT_BATCH {
script:
def args = task.ext.args ?: ''
// execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
// input pair is assumed to have same extension if both exist
def is_cram = tumor.Extension == "cram" ? true : false
def tumor_out = is_cram ? tumor.BaseName + ".bam" : "${tumor}"
def tumor_exists = tumor ? true : false
def normal_exists = normal ? true : false
// execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
def tumor_cram = tumor_exists && tumor.Extension == "cram" ? true : false
def normal_cram = normal_exists && normal.Extension == "cram" ? true : false
def tumor_bam = tumor_exists && tumor.Extension == "bam" ? true : false
def normal_bam = normal_exists && normal.Extension == "bam" ? true : false
def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}"
// do not run samtools on normal samples in tumor_only mode
def normal_exists = normal ? true: false
// tumor_only mode does not need fasta & target
// instead it requires a pre-computed reference.cnn which is built from fasta & target
def (normal_out, normal_args, fasta_args) = ["", "", ""]
def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : ""
if (normal_exists){
def normal_prefix = normal.BaseName
normal_out = is_cram ? "${normal_prefix}" + ".bam" : "${normal}"
normal_args = normal_prefix ? "--normal $normal_out" : ""
normal_out = normal_cram ? "${normal_prefix}" + ".bam" : "${normal}"
fasta_args = fasta ? "--fasta $fasta" : ""
// germline mode
// normal samples must be input without a flag
// requires flag --normal to be empty []
if(!tumor_exists){
tumor_out = "${normal_prefix}" + ".bam"
normal_args = "--normal "
}
// somatic mode
else {
normal_args = normal_prefix ? "--normal $normal_out" : ""
}
}
def target_args = targets ? "--targets $targets" : ""
def reference_args = reference ? "--reference $reference" : ""
// somatic_mode cram_input
if (tumor_cram && normal_cram){
"""
if $is_cram; then
samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out
if $normal_exists; then
samtools view -T $fasta $normal -@ $task.cpus -o $normal_out
fi
fi
samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out
samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $normal_out
cnvkit.py \\
batch \\
$tumor_out \\
$normal_args \\
$fasta_args \\
$reference_args \\
$target_args \\
--processes $task.cpus \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
END_VERSIONS
"""
}
// somatic_mode bam_input
else if (tumor_bam && normal_bam){
"""
cnvkit.py \\
batch \\
$tumor_out \\
@ -72,4 +107,89 @@ process CNVKIT_BATCH {
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
END_VERSIONS
"""
}
// tumor_only_mode cram_input
else if(tumor_cram && !normal_exists){
"""
samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out
cnvkit.py \\
batch \\
$tumor_out \\
$normal_args \\
$fasta_args \\
$reference_args \\
$target_args \\
--processes $task.cpus \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
END_VERSIONS
"""
}
// tumor_only bam_input
else if(tumor_bam && !normal_exists){
"""
cnvkit.py \\
batch \\
$tumor_out \\
$normal_args \\
$fasta_args \\
$reference_args \\
$target_args \\
--processes $task.cpus \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
END_VERSIONS
"""
}
// germline mode cram_input
// normal_args must be --normal []
else if (normal_cram && !tumor_exists){
"""
samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $tumor_out
cnvkit.py \\
batch \\
$tumor_out \\
$normal_args \\
$fasta_args \\
$reference_args \\
$target_args \\
--processes $task.cpus \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
END_VERSIONS
"""
}
// germline mode bam_input
else if (normal_bam && !tumor_exists){
"""
cnvkit.py \\
batch \\
$tumor_out \\
$normal_args \\
$fasta_args \\
$reference_args \\
$target_args \\
--processes $task.cpus \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
END_VERSIONS
"""
}
}

4
modules/cnvkit/batch/meta.yml
View file

@ -29,6 +29,10 @@ input:
type: file
description: |
Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)
- fasta_fai:
type: file
description: |
Input reference genome fasta index (optional, but recommended for cram_input)
- targetfile:
type: file
description: |

9
modules/cnvkit/reference/main.nf
View file

@ -1,5 +1,5 @@
process CNVKIT_REFERENCE {
tag "$reference"
tag "$fasta"
label 'process_low'
conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null)
@ -13,14 +13,15 @@ process CNVKIT_REFERENCE {
path antitargets
output:
path("*.cnn") , emit: cnn
path "versions.yml" , emit: versions
path "*.cnn" , emit: cnn
path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: targets.BaseName
"""
cnvkit.py \\
@ -28,7 +29,7 @@ process CNVKIT_REFERENCE {
--fasta $fasta \\
--targets $targets \\
--antitargets $antitargets \\
--output reference.cnn \\
--output ${prefix}.reference.cnn \\
$args
cat <<-END_VERSIONS > versions.yml

38
modules/deeptools/bamcoverage/main.nf
View file

@ -2,13 +2,15 @@ process DEEPTOOLS_BAMCOVERAGE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::deeptools=3.5.1" : null)
conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0':
'quay.io/biocontainers/deeptools:3.5.1--py_0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0':
'quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0' }"
input:
tuple val(meta), path(input), path(input_index)
path(fasta)
path(fasta_fai)
output:
tuple val(meta), path("*.bigWig") , emit: bigwig, optional: true
@ -22,9 +24,35 @@ process DEEPTOOLS_BAMCOVERAGE {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}.bigWig"
// cram_input is currently not working with deeptools
// therefore it's required to convert cram to bam first
def is_cram = input.Extension == "cram" ? true : false
def input_out = is_cram ? input.BaseName + ".bam" : "${input}"
def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : ""
if (is_cram){
"""
samtools view -T $fasta $input $fai_reference -@ $task.cpus -o $input_out
samtools index -b $input_out -@ $task.cpus
bamCoverage \\
--bam $input_out \\
$args \\
--numberOfProcessors ${task.cpus} \\
--outFileName ${prefix}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
END_VERSIONS
"""
}
else {
"""
bamCoverage \\
--bam $input \\
--bam $input_out \\
$args \\
--numberOfProcessors ${task.cpus} \\
--outFileName ${prefix}
@ -34,4 +62,6 @@ process DEEPTOOLS_BAMCOVERAGE {
deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
END_VERSIONS
"""
}
}

9
modules/deeptools/bamcoverage/meta.yml
View file

@ -25,6 +25,14 @@ input:
type: file
description: BAM/CRAM index file
pattern: "*.{bai,crai}"
- fasta:
type: file
description: Reference file the CRAM file was created with (required with CRAM input)
pattern: "*.{fasta,fa}"
- fasta_fai:
type: file
description: Index of the reference file (optional, but recommended)
pattern: "*.{fai}"
output:
- meta:
@ -47,3 +55,4 @@ output:
authors:
- "@FriederikeHanssen"
- "@SusiJo"

4
modules/ensemblvep/Dockerfile
View file

@ -11,8 +11,8 @@ RUN conda env create -f /environment.yml && conda clean -a
# Setup default ARG variables
ARG GENOME=GRCh38
ARG SPECIES=homo_sapiens
ARG VEP_VERSION=104
ARG VEP_TAG=104.3
ARG VEP_VERSION=105
ARG VEP_TAG=105.0
# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/nf-core-vep-${VEP_TAG}/bin:$PATH

12
modules/ensemblvep/build.sh
View file

@ -20,9 +20,9 @@ build_push() {
docker push nfcore/vep:${VEP_TAG}.${GENOME}
}
build_push "GRCh37" "homo_sapiens" "104" "104.3"
build_push "GRCh38" "homo_sapiens" "104" "104.3"
build_push "GRCm38" "mus_musculus" "102" "104.3"
build_push "GRCm39" "mus_musculus" "104" "104.3"
build_push "CanFam3.1" "canis_lupus_familiaris" "104" "104.3"
build_push "WBcel235" "caenorhabditis_elegans" "104" "104.3"
build_push "GRCh37" "homo_sapiens" "105" "105.0"
build_push "GRCh38" "homo_sapiens" "105" "105.0"
build_push "GRCm38" "mus_musculus" "102" "105.0"
build_push "GRCm39" "mus_musculus" "105" "105.0"
build_push "CanFam3.1" "canis_lupus_familiaris" "104" "105.0"
build_push "WBcel235" "caenorhabditis_elegans" "105" "105.0"

4
modules/ensemblvep/environment.yml
View file

@ -1,10 +1,10 @@
# You can use this file to create a conda environment for this module:
# conda env create -f environment.yml
name: nf-core-vep-104.3
name: nf-core-vep-105.0
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- bioconda::ensembl-vep=104.3
- bioconda::ensembl-vep=105.0

4
modules/ensemblvep/main.nf
View file

@ -13,6 +13,7 @@ process ENSEMBLVEP {
val species
val cache_version
path cache
path fasta
path extra_files
output:
@ -27,6 +28,8 @@ process ENSEMBLVEP {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep"
def reference = fasta ? "--fasta $fasta" : ""
"""
mkdir $prefix
@ -34,6 +37,7 @@ process ENSEMBLVEP {
-i $vcf \\
-o ${prefix}.ann.vcf \\
$args \\
$reference \\
--assembly $genome \\
--species $species \\
--cache \\

5
modules/ensemblvep/meta.yml
View file

@ -36,6 +36,11 @@ input:
type: file
description: |
path to VEP cache (optional)
- fasta:
type: file
description: |
reference FASTA file (optional)
pattern: "*.{fasta,fa}"
- extra_files:
type: tuple
description: |

7
modules/filtlong/main.nf
View file

@ -11,7 +11,7 @@ process FILTLONG {
tuple val(meta), path(shortreads), path(longreads)
output:
tuple val(meta), path("${meta.id}_lr_filtlong.fastq.gz"), emit: reads
tuple val(meta), path("*.fastq.gz"), emit: reads
path "versions.yml" , emit: versions
when:
@ -20,13 +20,14 @@ process FILTLONG {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def short_reads = meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
if ("$longreads" == "${prefix}.fastq.gz") error "Longread FASTQ input and output names are the same, set prefix in module configuration to disambiguate!"
"""
filtlong \\
$short_reads \\
$args \\
$longreads \\
| gzip -n > ${prefix}_lr_filtlong.fastq.gz
| gzip -n > ${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":

15
modules/gamma/main.nf → modules/gamma/gamma/main.nf
View file

@ -1,6 +1,6 @@
def VERSION = '2.1' // Version information not provided by tool on CLI
process GAMMA {
process GAMMA_GAMMA {
tag "$meta.id"
label 'process_low'
@ -26,13 +26,24 @@ process GAMMA {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
if [[ ${fasta} == *.gz ]]
then
FNAME=\$(basename ${fasta} .gz)
gunzip -f ${fasta}
GAMMA.py \\
$args \\
"\${FNAME}" \\
$db \\
$prefix
else
GAMMA.py \\
$args \\
$fasta \\
$db \\
$prefix
fi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gamma: $VERSION

3
modules/gamma/meta.yml → modules/gamma/gamma/meta.yml
View file

@ -1,4 +1,4 @@
name: "gamma"
name: "gamma_gamma"
description: Gene Allele Mutation Microbial Assessment
keywords:
- gamma
@ -61,3 +61,4 @@ output:
authors:
- "@sateeshperi"
- "@rastanton"
- "@jvhagey"

54
modules/gatk/indelrealigner/main.nf Normal file
View file

@ -0,0 +1,54 @@
process GATK_INDELREALIGNER {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk=3.5" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11':
'quay.io/biocontainers/gatk:3.5--hdfd78af_11' }"
input:
tuple val(meta), path(bam), path(bai), path(intervals)
path(fasta)
path(fai)
path(dict)
path(known_vcf)
output:
tuple val(meta), path("*.bam"), path("*.bai"), emit: bam
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 known = known_vcf ? "-known ${known_vcf}" : ""
if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
def avail_mem = 3
if (!task.memory) {
log.info '[GATK IndelRealigner] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk3 \\
-Xmx${avail_mem}g \\
-T IndelRealigner \\
-R ${fasta} \\
-I ${bam} \\
--targetIntervals ${intervals} \\
${known} \\
-o ${prefix}.bam \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk: \$(echo \$(gatk3 --version))
END_VERSIONS
"""
}

71
modules/gatk/indelrealigner/meta.yml Normal file
View file

@ -0,0 +1,71 @@
name: "gatk_indelrealigner"
description: Performs local realignment around indels to correct for mapping errors
keywords:
- bam
- vcf
- variant calling
- indel
- realignment
tools:
- "gatk":
description: "The full Genome Analysis Toolkit (GATK) framework, license restricted."
homepage: "https://gatk.broadinstitute.org/hc/en-us"
documentation: "https://github.com/broadinstitute/gatk-docs"
licence: "['https://software.broadinstitute.org/gatk/download/licensing', 'BSD', 'https://www.broadinstitute.org/gatk/about/#licensing']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Sorted and indexed BAM file
pattern: "*.bam"
- bai:
type: file
description: BAM index file
pattern: "*.bai"
- intervals:
type: file
description: Intervals file created by gatk3 RealignerTargetCreator
pattern: "*.{intervals,list}"
- fasta:
type: file
description: Reference file used to generate BAM file
pattern: ".{fasta,fa,fna}"
- fai:
type: file
description: Index of reference file used to generate BAM file
pattern: ".fai"
- dict:
type: file
description: GATK dict file for reference
pattern: ".dict"
- known_vcf:
type: file
description: Optional input VCF file(s) with known indels
pattern: ".vcf"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam:
type: file
description: Sorted and indexed BAM file with local realignment around variants
pattern: "*.bam"
- bai:
type: file
description: Output BAM Index file
pattern: "*.bai"
authors:
- "@jfy133"

53
modules/gatk/realignertargetcreator/main.nf Normal file
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@ -0,0 +1,53 @@
process GATK_REALIGNERTARGETCREATOR {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk=3.5" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11':
'quay.io/biocontainers/gatk:3.5--hdfd78af_11' }"
input:
tuple val(meta), path(input), path(index)
path fasta
path fai
path dict
path known_vcf
output:
tuple val(meta), path("*.intervals"), emit: intervals
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 known = known_vcf ? "-known ${known_vcf}" : ""
if ("$input" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
def avail_mem = 3
if (!task.memory) {
log.info '[GATK RealignerTargetCreator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk3 \\
-Xmx${avail_mem}g \\
-T RealignerTargetCreator \\
-nt ${task.cpus} \\
-I ${input} \\
-R ${fasta} \\
-o ${prefix}.intervals \\
${known} \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk: \$(echo \$(gatk3 --version))
END_VERSIONS
"""
}

64
modules/gatk/realignertargetcreator/meta.yml Normal file
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@ -0,0 +1,64 @@
name: "gatk_realignertargetcreator"
description: Generates a list of locations that should be considered for local realignment prior genotyping.
keywords:
- bam
- vcf
- variant calling
- indel
- realignment
- targets
tools:
- "gatk":
description: "The full Genome Analysis Toolkit (GATK) framework, license restricted."
homepage: "https://gatk.broadinstitute.org/hc/en-us"
documentation: "https://github.com/broadinstitute/gatk-docs"
licence: "['https://software.broadinstitute.org/gatk/download/licensing', 'BSD', 'https://www.broadinstitute.org/gatk/about/#licensing']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: Sorted and indexed BAM/CRAM/SAM file
pattern: "*.bam"
- index:
type: file
description: BAM index file
pattern: "*.bai"
- fasta:
type: file
description: Reference file used to generate BAM file
pattern: ".{fasta,fa,fna}"
- fai:
type: file
description: Index of reference file used to generate BAM file
pattern: ".fai"
- dict:
type: file
description: GATK dict file for reference
pattern: ".dict"
- known_vcf:
type: file
description: Optional input VCF file(s) with known indels
pattern: ".vcf"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- intervals:
type: file
description: File containg intervals that represent sites of extant and potential indels.
pattern: "*.intervals"
authors:
- "@jfy133"

63
modules/gatk/unifiedgenotyper/main.nf Normal file
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@ -0,0 +1,63 @@
process GATK_UNIFIEDGENOTYPER {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk=3.5" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11':
'quay.io/biocontainers/gatk:3.5--hdfd78af_11' }"
input:
tuple val(meta), path(input), path(index)
path fasta
path fai
path dict
path intervals
path contamination
path dbsnp
path comp
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def contamination_file = contamination ? "-contaminationFile ${contamination}" : ""
def dbsnp_file = dbsnp ? "--dbsnp ${dbsnp}" : ""
def comp_file = comp ? "--comp ${comp}" : ""
def intervals_file = intervals ? "--intervals ${intervals}" : ""
def avail_mem = 3
if (!task.memory) {
log.info '[GATK RealignerTargetCreator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk3 \\
-Xmx${avail_mem}g \\
-nt ${task.cpus} \\
-T UnifiedGenotyper \\
-I ${input} \\
-R ${fasta} \\
${contamination_file} \\
${dbsnp_file} \\
${comp_file} \\
${intervals_file} \\
-o ${prefix}.vcf \\
$args
gzip -n *.vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk: \$(echo \$(gatk3 --version))
END_VERSIONS
"""
}

73
modules/gatk/unifiedgenotyper/meta.yml Normal file
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@ -0,0 +1,73 @@
name: "gatk_unifiedgenotyper"
keywords:
- bam
- vcf
- variant calling
tools:
- "gatk":
description: "The full Genome Analysis Toolkit (GATK) framework, license restricted."
homepage: "https://gatk.broadinstitute.org/hc/en-us"
documentation: "https://github.com/broadinstitute/gatk-docs"
licence: "['https://software.broadinstitute.org/gatk/download/licensing', 'BSD', 'https://www.broadinstitute.org/gatk/about/#licensing']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: Sorted and indexed BAM/CRAM/SAM file
pattern: "*.bam"
- index:
type: file
description: BAM index file
pattern: "*.bai"
- fasta:
type: file
description: Reference file used to generate BAM file
pattern: ".{fasta,fa,fna}"
- fai:
type: file
description: Index of reference file used to generate BAM file
pattern: ".fai"
- dict:
type: file
description: GATK dict file for reference
pattern: ".dict"
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
pattern: "*.intervals"
- contamination:
type: file
description: Tab-separated file containing fraction of contamination in sequencing data (per sample) to aggressively remove
pattern: "*"
- dbsnps:
type: file
description: VCF file containing known sites (optional)
pattern: "*"
- comp:
type: file
description: Comparison VCF file (optional)
pattern: "*"
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: VCF file containing called variants
pattern: "*.vcf.gz"
authors:
- "@ilight1542"
- "@jfy133"

6
modules/gatk4/applybqsrspark/main.nf
View file

@ -2,10 +2,8 @@ process GATK4_APPLYBQSR_SPARK {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null)
container 'broadinstitute/gatk:4.2.6.1'
input:
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)

6
modules/gatk4/baserecalibratorspark/main.nf
View file

@ -2,10 +2,8 @@ process GATK4_BASERECALIBRATOR_SPARK {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null)
container 'broadinstitute/gatk:4.2.6.1'
input:
tuple val(meta), path(input), path(input_index), path(intervals)

51
modules/gatk4/calibratedragstrmodel/main.nf Normal file
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@ -0,0 +1,51 @@
process GATK4_CALIBRATEDRAGSTRMODEL {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam), path(bam_index), path(intervals)
path fasta
path fasta_fai
path dict
path strtablefile
output:
tuple val(meta), path("*.txt") , emit: dragstr_model
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 intervals_command = intervals ? "--intervals $intervals" : ""
def avail_mem = 3
if (!task.memory) {
log.info '[GATK CalibrateDragstrModel] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" CalibrateDragstrModel \\
--input $bam \\
--output ${prefix}.txt \\
--reference $fasta \\
--str-table-path $strtablefile \\
--threads $task.cpus \\
$intervals_command \\
--tmp-dir . \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

74
modules/gatk4/calibratedragstrmodel/meta.yml Normal file
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@ -0,0 +1,74 @@
name: gatk4_calibratedragstrmodel
description: estimates the parameters for the DRAGstr model
keywords:
- gatk4
- bam
- cram
- sam
- calibratedragstrmodel
tools:
- gatk4:
description:
Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
with a primary focus on variant discovery and genotyping. Its powerful processing engine
and high-performance computing features make it capable of taking on projects of any size.
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360057441571-CalibrateDragstrModel-BETA-
tool_dev_url: https://github.com/broadinstitute/gatk
doi: 10.1158/1538-7445.AM2017-3590
licence: ["Apache-2.0"]
input:
# Only when we have meta
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- bam_index:
type: file
description: index of the BAM/CRAM/SAM file
pattern: "*.{bai,crai,sai}"
- intervals:
type: file
description: BED file or interval list containing regions (optional)
pattern: "*.{bed,interval_list}"
- fasta:
type: file
description: The reference FASTA file
pattern: "*.{fasta,fa}"
- fasta_fai:
type: file
description: The index of the reference FASTA file
pattern: "*.fai"
- dict:
type: file
description: The sequence dictionary of the reference FASTA file
pattern: "*.dict"
- strtablefile:
type: file
description: The StrTableFile zip folder of the reference FASTA file
pattern: "*.zip"
output:
#Only when we have meta
- 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"
- dragstr_model:
type: file
description: The DragSTR model
pattern: "*.txt"
authors:
- "@nvnieuwk"

53
modules/gatk4/composestrtablefile/main.nf Normal file
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@ -0,0 +1,53 @@
process GATK4_COMPOSESTRTABLEFILE {
tag "$fasta"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
path(fasta)
path(fasta_fai)
path(dict)
output:
path "*.zip" , emit: str_table
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def avail_mem = 6
if (!task.memory) {
log.info '[GATK ComposeSTRTableFile] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" ComposeSTRTableFile \\
--reference $fasta \\
--output ${fasta.baseName}.zip \\
--tmp-dir . \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
stub:
"""
touch test.zip
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

43
modules/gatk4/composestrtablefile/meta.yml Normal file
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@ -0,0 +1,43 @@
name: "gatk4_composestrtablefile"
description: This tool looks for low-complexity STR sequences along the reference that are later used to estimate the Dragstr model during single sample auto calibration CalibrateDragstrModel.
keywords:
- gatk4
- composestrtablefile
tools:
- gatk4:
description:
Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
with a primary focus on variant discovery and genotyping. Its powerful processing engine
and high-performance computing features make it capable of taking on projects of any size.
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/4405451249819-ComposeSTRTableFile
tool_dev_url: https://github.com/broadinstitute/gatk
doi: 10.1158/1538-7445.AM2017-3590
licence: ["Apache-2.0"]
input:
- fasta:
type: file
description: FASTA reference file
pattern: "*.{fasta,fa}"
- fasta_fai:
type: file
description: index of the FASTA reference file
pattern: "*.fai"
- dict:
type: file
description: Sequence dictionary of the FASTA reference file
pattern: "*.dict"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- str_table:
type: file
description: A zipped folder containing the STR table files
pattern: "*.zip"
authors:
- "@nvnieuwk"

4
modules/gatk4/haplotypecaller/main.nf
View file

@ -8,7 +8,7 @@ process GATK4_HAPLOTYPECALLER {
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(input_index), path(intervals)
tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model)
path fasta
path fai
path dict
@ -28,6 +28,7 @@ process GATK4_HAPLOTYPECALLER {
def prefix = task.ext.prefix ?: "${meta.id}"
def dbsnp_command = dbsnp ? "--dbsnp $dbsnp" : ""
def interval_command = intervals ? "--intervals $intervals" : ""
def dragstr_command = dragstr_model ? "--dragstr-params-path $dragstr_model" : ""
def avail_mem = 3
if (!task.memory) {
@ -42,6 +43,7 @@ process GATK4_HAPLOTYPECALLER {
--reference $fasta \\
$dbsnp_command \\
$interval_command \\
$dragstr_command \\
--tmp-dir . \\
$args

4
modules/gatk4/haplotypecaller/meta.yml
View file

@ -32,6 +32,10 @@ input:
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- dragstr_model:
type: file
description: Text file containing the DragSTR model of the used BAM/CRAM file (optional)
pattern: "*.txt"
- fasta:
type: file
description: The reference fasta file

11
modules/gatk4/markduplicatesspark/main.nf
View file

@ -2,10 +2,8 @@ process GATK4_MARKDUPLICATES_SPARK {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'broadinstitute/gatk:4.2.3.0' }"
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null)
container 'broadinstitute/gatk:4.2.6.1'
input:
tuple val(meta), path(bam)
@ -15,6 +13,7 @@ process GATK4_MARKDUPLICATES_SPARK {
output:
tuple val(meta), path("${prefix}"), emit: output
tuple val(meta), path("*.metrics"), emit: metrics, optional: true
path "versions.yml" , emit: versions
when:
@ -25,6 +24,7 @@ process GATK4_MARKDUPLICATES_SPARK {
prefix = task.ext.prefix ?: "${meta.id}"
def input_list = bam.collect{"--input $it"}.join(' ')
def avail_mem = 3
if (!task.memory) {
log.info '[GATK MarkDuplicatesSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@ -32,8 +32,6 @@ process GATK4_MARKDUPLICATES_SPARK {
avail_mem = task.memory.giga
}
"""
export SPARK_USER=spark3
gatk --java-options "-Xmx${avail_mem}g" MarkDuplicatesSpark \\
$input_list \\
--output $prefix \\
@ -45,6 +43,7 @@ process GATK4_MARKDUPLICATES_SPARK {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
openjdk: \$(echo \$(java -version 2>&1) | grep version | sed 's/\"//g' | cut -f3 -d ' ')
END_VERSIONS
"""
}

1
modules/gatk4/markduplicatesspark/meta.yml
View file

@ -58,3 +58,4 @@ authors:
- "@ajodeh-juma"
- "@FriederikeHanssen"
- "@maxulysse"
- "@SusiJo"

1
modules/gatk4/mergevcfs/main.nf
View file

@ -13,6 +13,7 @@ process GATK4_MERGEVCFS {
output:
tuple val(meta), path('*.vcf.gz'), emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi
path "versions.yml" , emit: versions
when:

5
modules/gatk4/mergevcfs/meta.yml
View file

@ -35,6 +35,11 @@ output:
type: file
description: merged vcf file
pattern: "*.vcf.gz"
- tbi:
type: file
description: index files for the merged vcf files
pattern: "*.tbi"
- versions:
type: file
description: File containing software versions

52
modules/gatk4/reblockgvcf/main.nf Normal file
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@ -0,0 +1,52 @@
process GATK4_REBLOCKGVCF {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(gvcf), path(tbi), path(intervals)
path fasta
path fai
path dict
path dbsnp
path dbsnp_tbi
output:
tuple val(meta), path("*.rb.g.vcf.gz"), path("*.tbi") , emit: vcf
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def dbsnp_command = dbsnp ? "--dbsnp $dbsnp" : ""
def interval_command = intervals ? "--intervals $intervals" : ""
def avail_mem = 3
if (!task.memory) {
log.info '[GATK ReblockGVCF] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" ReblockGVCF \\
--variant $gvcf \\
--output ${prefix}.rb.g.vcf.gz \\
--reference $fasta \\
$dbsnp_command \\
$interval_command \\
--tmp-dir . \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

74
modules/gatk4/reblockgvcf/meta.yml Normal file
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@ -0,0 +1,74 @@
name: "gatk4_reblockgvcf"
description: Condenses homRef blocks in a single-sample GVCF
keywords:
- gatk4
- reblockgvcf
- gvcf
tools:
- gatk4:
description: |
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
with a primary focus on variant discovery and genotyping. Its powerful processing engine
and high-performance computing features make it capable of taking on projects of any size.
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ["Apache-2.0"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- gvcf:
type: file
description: GVCF file created using HaplotypeCaller using the '-ERC GVCF' or '-ERC BP_RESOLUTION' mode
pattern: "*.{vcf,gvcf}.gz"
- tbi:
type: file
description: Index of the GVCF file
pattern: "*.tbi"
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
- dbsnp:
type: file
description: VCF file containing known sites (optional)
- dbsnp_tbi:
type: file
description: VCF index of dbsnp (optional)
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"
- gvcf:
type: file
description: Filtered GVCF
pattern: "*rb.g.vcf.gz"
- tbi:
type: file
description: Index of the filtered GVCF
pattern: "*rb.g.vcf.gz.tbi"
authors:
- "@nvnieuwk"

42
modules/kat/hist/main.nf Normal file
View file

@ -0,0 +1,42 @@
process KAT_HIST {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::kat=2.4.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/kat:2.4.2--py38hfc5f9d8_2':
'quay.io/biocontainers/kat:2.4.2--py38hfc5f9d8_2' }"
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*.hist") , emit: hist
tuple val(meta), path("*.hist.dist_analysis.json"), emit: json
tuple val(meta), path("*.png") , emit: png , optional: true
tuple val(meta), path("*.ps") , emit: ps , optional: true
tuple val(meta), path("*.pdf") , emit: pdf , optional: true
tuple val(meta), path("*-hash.jf*") , emit: jellyfish_hash, optional: true
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}"
"""
kat hist \\
--threads $task.cpus \\
--output_prefix ${prefix}.hist \\
$args \\
$reads
ls -l
cat <<-END_VERSIONS > versions.yml
"${task.process}":
kat: \$( kat hist --version | sed 's/kat //' )
END_VERSIONS
"""
}

64
modules/kat/hist/meta.yml Normal file
View file

@ -0,0 +1,64 @@
name: "kat_hist"
description: Creates a histogram of the number of distinct k-mers having a given frequency.
keywords:
- k-mer
- histogram
- count
tools:
- "kat":
description: "KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts"
homepage: https://www.earlham.ac.uk/kat-tools
documentation: https://kat.readthedocs.io/en/latest/index.html
tool_dev_url: https://github.com/TGAC/KAT
doi: http://bioinformatics.oxfordjournals.org/content/early/2016/10/20/bioinformatics.btw663.abstract
licence: "['GPL v3']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
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"
- hist:
type: file
description: KAT histogram of k-mer counts
pattern: "*.hist"
- json:
type: file
description: KAT histogram summary of distance analysis
pattern: "*.hist.dist_analysis.json"
- png:
type: file
description: KAT plot of k-mer histogram in PNG format
pattern: "*.png"
- ps:
type: file
description: KAT plot of k-mer histogram in PS format
pattern: "*.ps"
- pdf:
type: file
description: KAT plot of k-mer histogram in PDF format
pattern: "*.pdf"
- jellyfish_hash:
type: file
description: Jellyfish hash file
pattern: "*-hist.jf*"
authors:
- "@mahesh-panchal"

8
modules/mash/screen/main.nf
View file

@ -8,8 +8,8 @@ process MASH_SCREEN {
'quay.io/biocontainers/mash:2.3--he348c14_1' }"
input:
tuple val(meta), path(query_sketch)
path fastx_db
tuple val(meta), path(query)
path sequences_sketch
output:
tuple val(meta), path("*.screen"), emit: screen
@ -26,8 +26,8 @@ process MASH_SCREEN {
screen \\
$args \\
-p $task.cpus \\
$query_sketch \\
$fastx_db \\
$sequences_sketch \\
$query \\
> ${prefix}.screen
cat <<-END_VERSIONS > versions.yml

9
modules/mash/screen/meta.yml
View file

@ -20,13 +20,14 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- query_sketch:
- query:
type: file
description: MinHash sketch of query sequences
pattern: "*.msh"
- fastx_db:
description: Query sequences
pattern: "*.fastq.gz"
- sequence_sketch:
type: file
description: Sequence files to match against
pattern: "*.msh"
output:
- meta:

39
modules/mosdepth/main.nf
View file

@ -10,17 +10,21 @@ process MOSDEPTH {
input:
tuple val(meta), path(bam), path(bai)
path bed
val window_size
path fasta
output:
tuple val(meta), path('*.global.dist.txt') , emit: global_txt
tuple val(meta), path('*.region.dist.txt') , emit: regions_txt , optional:true
tuple val(meta), path('*.summary.txt') , emit: summary_txt
tuple val(meta), path('*.per-base.d4') , emit: d4 , optional:true
tuple val(meta), path('*.per-base.bed.gz') , emit: per_base_bed, optional:true
tuple val(meta), path('*.per-base.bed.gz.csi'), emit: per_base_csi, optional:true
tuple val(meta), path('*.regions.bed.gz') , emit: regions_bed , optional:true
tuple val(meta), path('*.regions.bed.gz.csi') , emit: regions_csi , optional:true
tuple val(meta), path('*.region.dist.txt') , optional:true, emit: regions_txt
tuple val(meta), path('*.per-base.d4') , optional:true, emit: per_base_d4
tuple val(meta), path('*.per-base.bed.gz') , optional:true, emit: per_base_bed
tuple val(meta), path('*.per-base.bed.gz.csi') , optional:true, emit: per_base_csi
tuple val(meta), path('*.regions.bed.gz') , optional:true, emit: regions_bed
tuple val(meta), path('*.regions.bed.gz.csi') , optional:true, emit: regions_csi
tuple val(meta), path('*.quantized.bed.gz') , optional:true, emit: quantized_bed
tuple val(meta), path('*.quantized.bed.gz.csi') , optional:true, emit: quantized_csi
tuple val(meta), path('*.thresholds.bed.gz') , optional:true, emit: thresholds_bed
tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi
path "versions.yml" , emit: versions
when:
@ -29,19 +33,24 @@ process MOSDEPTH {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if (window_size) {
interval = "--by ${window_size}"
} else if ( bed ) {
interval = "--by ${bed}"
} else {
interval = ""
def reference = fasta ? "--fasta ${fasta}" : ""
def interval = bed ? "--by ${bed}" : ""
if (bed && args.contains("--by")) {
exit 1, "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition"
}
if (!bed && args.contains("--thresholds")) {
exit 1, "'--thresholds' can only be specified in conjunction with '--by'"
}
"""
mosdepth \\
--threads $task.cpus \\
$interval \\
$reference \\
$args \\
$prefix \\
$bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
@ -59,6 +68,10 @@ process MOSDEPTH {
touch ${prefix}.per-base.bed.gz.csi
touch ${prefix}.regions.bed.gz
touch ${prefix}.regions.bed.gz.csi
touch ${prefix}.quantized.bed.gz
touch ${prefix}.quantized.bed.gz.csi
touch ${prefix}.thresholds.bed.gz
touch ${prefix}.thresholds.bed.gz.csi
cat <<-END_VERSIONS > versions.yml
"${task.process}":

29
modules/mosdepth/meta.yml
View file

@ -30,10 +30,10 @@ input:
type: file
description: BED file with intersected intervals
pattern: "*.{bed}"
- window_size:
type: integer
description: Window size
pattern: "[0-9]+"
- fasta:
type: file
description: Reference genome FASTA file
pattern: "*.{fa,fasta}"
output:
- meta:
type: map
@ -60,6 +60,10 @@ output:
type: file
description: Index file for BED file with per-base coverage
pattern: "*.{per-base.bed.gz.csi}"
- per_base_d4:
type: file
description: D4 file with per-base coverage
pattern: "*.{per-base.d4}"
- regions_bed:
type: file
description: BED file with per-region coverage
@ -68,6 +72,22 @@ output:
type: file
description: Index file for BED file with per-region coverage
pattern: "*.{regions.bed.gz.csi}"
- quantized_bed:
type: file
description: BED file with binned coverage
pattern: "*.{quantized.bed.gz}"
- quantized_csi:
type: file
description: Index file for BED file with binned coverage
pattern: "*.{quantized.bed.gz.csi}"
- thresholds_bed:
type: file
description: BED file with the number of bases in each region that are covered at or above each threshold
pattern: "*.{thresholds.bed.gz}"
- thresholds_csi:
type: file
description: Index file for BED file with threshold coverage
pattern: "*.{thresholds.bed.gz.csi}"
- versions:
type: file
description: File containing software versions
@ -76,3 +96,4 @@ authors:
- "@joseespinosa"
- "@drpatelh"
- "@ramprasadn"
- "@matthdsm"

10
modules/multiqc/main.nf
View file

@ -7,7 +7,8 @@ process MULTIQC {
'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
input:
path multiqc_files
path multiqc_files, stageAs: "?/*"
tuple path(multiqc_config), path(multiqc_logo)
output:
path "*multiqc_report.html", emit: report
@ -20,8 +21,13 @@ process MULTIQC {
script:
def args = task.ext.args ?: ''
def config = multiqc_config ? "--config $multiqc_config" : ''
"""
multiqc -f $args .
multiqc \\
--force \\
$config \\
$args \\
.
cat <<-END_VERSIONS > versions.yml
"${task.process}":

8
modules/multiqc/meta.yml
View file

@ -17,6 +17,14 @@ input:
type: file
description: |
List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
- multiqc_config:
type: file
description: Config yml for MultiQC
pattern: "*.{yml,yaml}"
- multiqc_logo:
type: file
description: Logo file for MultiQC
pattern: "*.{png}"
output:
- report:
type: file

6
modules/picard/addorreplacereadgroups/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

6
modules/picard/cleansam/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_CLEANSAM {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

6
modules/picard/collecthsmetrics/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

6
modules/picard/collectmultiplemetrics/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

6
modules/picard/collectwgsmetrics/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

6
modules/picard/createsequencedictionary/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input:
tuple val(meta), path(fasta)

6
modules/picard/crosscheckfingerprints/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_CROSSCHECKFINGERPRINTS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input:
tuple val(meta), path(input1)

6
modules/picard/filtersamreads/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input:
tuple val(meta), path(bam), path(readlist)

6
modules/picard/fixmateinformation/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_FIXMATEINFORMATION {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

6
modules/picard/liftovervcf/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_LIFTOVERVCF {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input:
tuple val(meta), path(input_vcf)

6
modules/picard/markduplicates/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

6
modules/picard/mergesamfiles/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input:
tuple val(meta), path(bams)

6
modules/picard/sortsam/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_SORTSAM {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

6
modules/picard/sortvcf/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_SORTVCF {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
input:
tuple val(meta), path(vcf)

51
modules/rhocall/annotate/main.nf Normal file
View file

@ -0,0 +1,51 @@
process RHOCALL_ANNOTATE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::rhocall=0.5.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/rhocall:0.5.1--py39hbf8eff0_0':
'quay.io/biocontainers/rhocall:0.5.1--py39hbf8eff0_0' }"
input:
tuple val(meta), path(vcf), path(tbi)
tuple val(meta), path(roh)
path bed
output:
tuple val(meta), path("*_rhocall.vcf"), emit: vcf
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def az_bed = bed ? "-b ${bed}" : ''
"""
rhocall \\
annotate \\
$args \\
$az_bed \\
-r $roh \\
-o ${prefix}_rhocall.vcf \\
$vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' )
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_rhocall.vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' )
END_VERSIONS
"""
}

54
modules/rhocall/annotate/meta.yml Normal file
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@ -0,0 +1,54 @@
name: "rhocall_annotate"
description: "Markup VCF file using rho-calls."
keywords:
- roh
- rhocall
tools:
- "rhocall":
description: "Call regions of homozygosity and make tentative UPD calls."
homepage: "https://github.com/dnil/rhocall"
documentation: "https://github.com/dnil/rhocall"
tool_dev_url: "https://github.com/dnil"
doi: ""
licence: "['GPL v3']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: vcf file
pattern: "*.{vcf,vcf.gz}"
- tbi:
type: file
description: vcf index file
pattern: "*.{tbi}"
- roh:
type: file
description: Bcftools roh style TSV file with CHR,POS,AZ,QUAL
pattern: "*.{roh}"
- bed:
type: file
description: BED file with AZ windows.
pattern: "*.{bed}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: vcf file
pattern: "*.{vcf,vcf.gz}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@ramprasadn"

55
modules/snippy/run/main.nf Normal file
View file

@ -0,0 +1,55 @@
process SNIPPY_RUN {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2' :
'quay.io/biocontainers/snippy:4.6.0--hdfd78af_2' }"
input:
tuple val(meta), path(reads)
path reference
output:
tuple val(meta), path("${prefix}/${prefix}.tab") , emit: tab
tuple val(meta), path("${prefix}/${prefix}.csv") , emit: csv
tuple val(meta), path("${prefix}/${prefix}.html") , emit: html
tuple val(meta), path("${prefix}/${prefix}.vcf") , emit: vcf
tuple val(meta), path("${prefix}/${prefix}.bed") , emit: bed
tuple val(meta), path("${prefix}/${prefix}.gff") , emit: gff
tuple val(meta), path("${prefix}/${prefix}.bam") , emit: bam
tuple val(meta), path("${prefix}/${prefix}.bam.bai") , emit: bai
tuple val(meta), path("${prefix}/${prefix}.log") , emit: log
tuple val(meta), path("${prefix}/${prefix}.aligned.fa") , emit: aligned_fa
tuple val(meta), path("${prefix}/${prefix}.consensus.fa") , emit: consensus_fa
tuple val(meta), path("${prefix}/${prefix}.consensus.subs.fa"), emit: consensus_subs_fa
tuple val(meta), path("${prefix}/${prefix}.raw.vcf") , emit: raw_vcf
tuple val(meta), path("${prefix}/${prefix}.filt.vcf") , emit: filt_vcf
tuple val(meta), path("${prefix}/${prefix}.vcf.gz") , emit: vcf_gz
tuple val(meta), path("${prefix}/${prefix}.vcf.gz.csi") , emit: vcf_csi
tuple val(meta), path("${prefix}/${prefix}.txt") , emit: txt
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def read_inputs = meta.single_end ? "--se ${reads[0]}" : "--R1 ${reads[0]} --R2 ${reads[1]}"
"""
snippy \\
$args \\
--cpus $task.cpus \\
--outdir $prefix \\
--reference $reference \\
--prefix $prefix \\
$read_inputs
cat <<-END_VERSIONS > versions.yml
"${task.process}":
snippy: \$(echo \$(snippy --version 2>&1) | sed 's/snippy //')
END_VERSIONS
"""
}

110
modules/snippy/run/meta.yml Normal file
View file

@ -0,0 +1,110 @@
name: snippy_run
description: Rapid haploid variant calling
keywords:
- variant
- fastq
- bacteria
tools:
- snippy:
description: "Rapid bacterial SNP calling and core genome alignments"
homepage: "https://github.com/tseemann/snippy"
documentation: "https://github.com/tseemann/snippy"
tool_dev_url: "https://github.com/tseemann/snippy"
doi: ""
licence: "['GPL v2']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
- index:
type: file
description: Reference genome in GenBank (preferred) or FASTA format
pattern: "*.{gbk,gbk.gz,fa,fa.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"
- tab:
type: file
description: A simple tab-separated summary of all the variants
pattern: "*.tab"
- csv:
type: file
description: A comma-separated version of the .tab file
pattern: "*.csv"
- html:
type: file
description: A HTML version of the .tab file
pattern: "*.html"
- vcf:
type: file
description: The final annotated variants in VCF format
pattern: "*.vcf"
- bed:
type: file
description: The variants in BED format
pattern: "*.bed"
- gff:
type: file
description: The variants in GFF3 format
pattern: "*.gff"
- bam:
type: file
description: The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates.
pattern: "*.bam"
- bai:
type: file
description: Index for the .bam file
pattern: "*.bam.bai"
- log:
type: file
description: A log file with the commands run and their outputs
pattern: "*.log"
- aligned_fa:
type: file
description: A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants)
pattern: "*.aligned.fa"
- consensus_fa:
type: file
description: A version of the reference genome with all variants instantiated
pattern: "*.consensus.fa"
- consensus_subs_fa:
type: file
description: A version of the reference genome with only substitution variants instantiated
pattern: "*.consensus.subs.fa"
- raw_vcf:
type: file
description: The unfiltered variant calls from Freebayes
pattern: "*.raw.vcf"
- filt_vcf:
type: file
description: The filtered variant calls from Freebayes
pattern: "*.filt.vcf"
- vcf_gz:
type: file
description: Compressed .vcf file via BGZIP
pattern: "*.vcf.gz"
- vcf_csi:
type: file
description: Index for the .vcf.gz via bcftools index
pattern: "*.vcf.gz.csi"
- txt:
type: file
description: Tab-separated columnar list of statistics
pattern: "*.txt"
authors:
- "@rpetit3"

9
modules/star/align/main.nf
View file

@ -2,11 +2,10 @@ process STAR_ALIGN {
tag "$meta.id"
label 'process_high'
// Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? 'bioconda::star=2.7.9a' : null)
conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/star:2.7.9a--h9ee0642_0' :
'quay.io/biocontainers/star:2.7.9a--h9ee0642_0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' :
'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' }"
input:
tuple val(meta), path(reads)
@ -67,6 +66,8 @@ process STAR_ALIGN {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
star: \$(STAR --version | sed -e "s/STAR_//g")
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
"""
}

9
modules/star/genomegenerate/main.nf
View file

@ -2,11 +2,10 @@ process STAR_GENOMEGENERATE {
tag "$fasta"
label 'process_high'
// Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? "bioconda::star=2.7.9a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1c4c32d87798d425c970ececfbadd155e7560277-0' :
'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1c4c32d87798d425c970ececfbadd155e7560277-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' :
'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' }"
input:
path fasta
@ -14,7 +13,7 @@ process STAR_GENOMEGENERATE {
output:
path "star" , emit: index
path "versions.yml" , emit: versions
path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when

16
modules/tiddit/cov/main.nf
View file

@ -2,17 +2,17 @@ process TIDDIT_COV {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::tiddit=2.12.1" : null)
conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0' :
'quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0' }"
'https://depot.galaxyproject.org/singularity/tiddit:3.0.0--py39h59fae87_1' :
'quay.io/biocontainers/tiddit:3.0.0--py39h59fae87_1' }"
input:
tuple val(meta), path(bam)
tuple val(meta), path(input)
path fasta
output:
tuple val(meta), path("*.tab"), optional: true, emit: cov
tuple val(meta), path("*.bed"), optional: true, emit: cov
tuple val(meta), path("*.wig"), optional: true, emit: wig
path "versions.yml" , emit: versions
@ -28,12 +28,12 @@ process TIDDIT_COV {
--cov \\
-o $prefix \\
$args \\
--bam $bam \\
--bam $input \\
$reference
cat <<-END_VERSIONS > versions.yml
"${task.process}":
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
END_VERSIONS
"""
@ -45,7 +45,7 @@ process TIDDIT_COV {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
END_VERSIONS
"""
}

2
modules/tiddit/cov/meta.yml
View file

@ -19,7 +19,7 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
- input:
type: file
description: BAM/CRAM file
pattern: "*.{bam,cram}"

27
modules/tiddit/sv/main.nf
View file

@ -2,20 +2,19 @@ process TIDDIT_SV {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::tiddit=2.12.1" : null)
conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0' :
'quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0' }"
'https://depot.galaxyproject.org/singularity/tiddit:3.0.0--py39h59fae87_1' :
'quay.io/biocontainers/tiddit:3.0.0--py39h59fae87_1' }"
input:
tuple val(meta), path(bam)
tuple val(meta), path(input), path(input_index)
path fasta
path fai
path bwa_index
output:
tuple val(meta), path("*.vcf") , emit: vcf
tuple val(meta), path("*.ploidy.tab") , emit: ploidy
tuple val(meta), path("*.signals.tab"), emit: signals
tuple val(meta), path("*.ploidies.tab"), emit: ploidy
path "versions.yml" , emit: versions
when:
@ -24,18 +23,19 @@ process TIDDIT_SV {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta ? "--ref $fasta" : ""
"""
[[ -d $bwa_index ]] && for i in $bwa_index/*; do [[ -f $fasta && ! "\$i" =~ .*"$fasta".* ]] && ln -s \$i ${fasta}.\${i##*.} || ln -s \$i .; done
tiddit \\
--sv \\
$args \\
--bam $bam \\
$reference \\
--bam $input \\
--ref $fasta \\
-o $prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
END_VERSIONS
"""
@ -43,12 +43,11 @@ process TIDDIT_SV {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf
touch ${prefix}.ploidy.tab
touch ${prefix}.signals.tab
touch ${prefix}.ploidies.tab
cat <<-END_VERSIONS > versions.yml
"${task.process}":
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
END_VERSIONS
"""
}

20
modules/tiddit/sv/meta.yml
View file

@ -17,14 +17,22 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: BAM/CRAM file
pattern: "*.{bam,cram}"
- index:
type: file
description: BAM/CRAM index file
pattern: "*.{bai,crai}"
- fasta:
type: file
description: Input FASTA file
pattern: "*.{fasta,fa}"
- fai:
- bwa_index:
type: file
description: FASTA index file
pattern: "*.{fai}"
description: BWA genome index files
pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
output:
- meta:
type: map
@ -38,11 +46,7 @@ output:
- ploidy:
type: file
description: tab
pattern: "*.{ploidy.tab}"
- signals:
type: file
description: tab
pattern: "*.{signals.tab}"
pattern: "*.{ploidies.tab}"
- versions:
type: file
description: File containing software versions

8
modules/untar/main.nf
View file

@ -21,12 +21,18 @@ process UNTAR {
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
untar = archive.toString() - '.tar.gz'
"""
mkdir output
tar \\
-C output --strip-components 1 \\
-xzvf \\
$args \\
$archive \\
$args2 \\
$args2
mv output ${untar}
cat <<-END_VERSIONS > versions.yml
"${task.process}":

67
modules/vsearch/usearchglobal/main.nf Normal file
View file

@ -0,0 +1,67 @@
process VSEARCH_USEARCHGLOBAL {
tag "${meta.id}"
label 'process_low'
conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--h95f258a_0':
'quay.io/biocontainers/vsearch:2.21.1--h95f258a_0' }"
input:
tuple val(meta), path(queryfasta)
path db
val idcutoff
val outoption
val user_columns
output:
tuple val(meta), path('*.aln') , optional: true, emit: aln
tuple val(meta), path('*.biom') , optional: true, emit: biom
tuple val(meta), path('*.lca') , optional: true, emit: lca
tuple val(meta), path('*.mothur') , optional: true, emit: mothur
tuple val(meta), path('*.otu') , optional: true, emit: otu
tuple val(meta), path('*.sam') , optional: true, emit: sam
tuple val(meta), path('*.tsv') , optional: true, emit: tsv
tuple val(meta), path('*.txt') , optional: true, emit: txt
tuple val(meta), path('*.uc') , optional: true, emit: uc
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 columns = user_columns ? "--userfields ${user_columns}" : ''
switch ( outoption ) {
case "alnout": outfmt = "--alnout"; out_ext = 'aln'; break
case "biomout": outfmt = "--biomout"; out_ext = 'biom'; break
case "blast6out": outfmt = "--blast6out"; out_ext = 'txt'; break
case "mothur_shared_out": outfmt = "--mothur_shared_out"; out_ext = 'mothur'; break
case "otutabout": outfmt = "--otutabout"; out_ext = 'otu'; break
case "samout": outfmt = "--samout"; out_ext = 'sam'; break
case "uc": outfmt = "--uc"; out_ext = 'uc'; break
case "userout": outfmt = "--userout"; out_ext = 'tsv'; break
case "lcaout": outfmt = "--lcaout"; out_ext = 'lca'; break
default:
outfmt = "--alnout";
out_ext = 'aln';
log.warn("Unknown output file format provided (${outoption}): selecting pairwise alignments (alnout)");
break
}
"""
vsearch \\
--usearch_global $queryfasta \\
--db $db \\
--id $idcutoff \\
--threads $task.cpus \\
$args \\
${columns} \\
${outfmt} ${prefix}.${out_ext}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
vsearch: \$(vsearch --version 2>&1 | head -n 1 | sed 's/vsearch //g' | sed 's/,.*//g' | sed 's/^v//' | sed 's/_.*//')
END_VERSIONS
"""
}

83
modules/vsearch/usearchglobal/meta.yml Normal file
View file

@ -0,0 +1,83 @@
name: "vsearch_usearchglobal"
description: Compare target sequences to fasta-formatted query sequences using global pairwise alignment.
keywords:
- vsearch
- usearch
- alignment
- fasta
tools:
- "vsearch":
description: "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)"
homepage: "https://github.com/torognes/vsearch"
documentation: "None"
tool_dev_url: "https://github.com/torognes/vsearch"
doi: "doi: 10.7717/peerj.2584"
licence: "['GPL v3-or-later OR BSD-2-clause']"
input:
- meta:
type: map
description: Groovy Map containing sample information e.g. [ id:'test' ]
- queryfasta:
type: file
description: Query sequences in FASTA format
pattern: "*.{fasta,fa,fna,faa}"
- db:
type: file
description: Reference database file in FASTA or UDB format
pattern: "*"
- idcutoff:
type: real
description: Reject the sequence match if the pairwise identity is lower than the given id cutoff value (value ranging from 0.0 to 1.0 included)
- outoption:
type: string
description: Specify the type of output file to be generated by selecting one of the vsearch output file options
pattern: "alnout|biomout|blast6out|mothur_shared_out|otutabout|samout|uc|userout|lcaout"
- user_columns:
type: string
description: If using the `userout` option, specify which columns to include in output, with fields separated with `+` (e.g. query+target+id). See USEARCH manual for valid options. For other output options, use an empty string.
output:
- aln:
type: file
description: Results in pairwise alignment format
pattern: "*.{aln}"
- biom:
type: file
description: Results in an OTU table in the biom version 1.0 file format
pattern: "*.{biom}"
- lca:
type: file
description: Last common ancestor (LCA) information about the hits of each query in tab-separated format
pattern: "*.{lca}"
- mothur:
type: file
description: Results in an OTU table in the mothur ’shared’ tab-separated plain text file format
pattern: "*.{mothur}"
- otu:
type: file
description: Results in an OTU table in the classic tab-separated plain text format
pattern: "*.{otu}"
- sam:
type: file
description: Results written in sam format
pattern: "*.{sam}"
- tsv:
type: file
description: Results in tab-separated output, columns defined by user
pattern: "*.{tsv}"
- txt:
type: file
description: Tab delimited results in blast-like tabular format
pattern: "*.{txt}"
- uc:
type: file
description: Tab delimited results in a uclust-like format with 10 columns
pattern: "*.{uc}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@jtangrot"

50
tests/config/pytest_modules.yml
View file

@ -166,6 +166,10 @@ bcftools/reheader:
- modules/bcftools/reheader/**
- tests/modules/bcftools/reheader/**
bcftools/roh:
- modules/bcftools/roh/**
- tests/modules/bcftools/roh/**
bcftools/sort:
- modules/bcftools/sort/**
- tests/modules/bcftools/sort/**
@ -707,9 +711,21 @@ freebayes:
- modules/freebayes/**
- tests/modules/freebayes/**
gamma:
- modules/gamma/**
- tests/modules/gamma/**
gamma/gamma:
- modules/gamma/gamma/**
- tests/modules/gamma/gamma/**
gatk/indelrealigner:
- modules/gatk/indelrealigner/**
- tests/modules/gatk/indelrealigner/**
gatk/realignertargetcreator:
- modules/gatk/realignertargetcreator/**
- tests/modules/gatk/realignertargetcreator/**
gatk/unifiedgenotyper:
- modules/gatk/unifiedgenotyper/**
- tests/modules/gatk/unifiedgenotyper/**
gatk4/applybqsr:
- modules/gatk4/applybqsr/**
@ -739,6 +755,10 @@ gatk4/calculatecontamination:
- modules/gatk4/calculatecontamination/**
- tests/modules/gatk4/calculatecontamination/**
gatk4/calibratedragstrmodel:
- modules/gatk4/calibratedragstrmodel/**
- tests/modules/gatk4/calibratedragstrmodel/**
gatk4/cnnscorevariants:
- modules/gatk4/cnnscorevariants/**
- tests/modules/gatk4/cnnscorevariants/**
@ -747,6 +767,10 @@ gatk4/combinegvcfs:
- modules/gatk4/combinegvcfs/**
- tests/modules/gatk4/combinegvcfs/**
gatk4/composestrtablefile:
- modules/gatk4/composestrtablefile/**
- tests/modules/gatk4/composestrtablefile/**
gatk4/createsequencedictionary:
- modules/gatk4/createsequencedictionary/**
- tests/modules/gatk4/createsequencedictionary/**
@ -835,6 +859,10 @@ gatk4/mutect2:
- modules/gatk4/mutect2/**
- tests/modules/gatk4/mutect2/**
gatk4/reblockgvcf:
- modules/gatk4/reblockgvcf/**
- tests/modules/gatk4/reblockgvcf/**
gatk4/revertsam:
- modules/gatk4/revertsam/**
- tests/modules/gatk4/revertsam/**
@ -1089,6 +1117,10 @@ kallistobustools/ref:
- modules/kallistobustools/ref/**
- tests/modules/kallistobustools/ref/**
kat/hist:
- modules/kat/hist/**
- tests/modules/kat/hist/**
khmer/normalizebymedian:
- modules/khmer/normalizebymedian/**
- tests/modules/khmer/normalizebymedian/**
@ -1627,6 +1659,10 @@ rgi/main:
- modules/rgi/main/**
- tests/modules/rgi/main/**
rhocall/annotate:
- modules/rhocall/annotate/**
- tests/modules/rhocall/annotate/**
rmarkdownnotebook:
- modules/rmarkdownnotebook/**
- tests/modules/rmarkdownnotebook/**
@ -1847,6 +1883,10 @@ snapaligner/index:
- modules/snapaligner/index/**
- tests/modules/snapaligner/index/**
snippy/run:
- modules/snippy/run/**
- tests/modules/snippy/run/**
snpdists:
- modules/snpdists/**
- tests/modules/snpdists/**
@ -2048,6 +2088,10 @@ vcftools:
- modules/vcftools/**
- tests/modules/vcftools/**
vsearch/usearchglobal:
- modules/vsearch/usearchglobal/**
- tests/modules/vsearch/usearchglobal/**
yara/index:
- modules/yara/index/**
- tests/modules/yara/index/**

11
tests/config/test_data.config
View file

@ -23,6 +23,8 @@ params {
test_bed12 = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed12"
baits_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/baits.bed"
reference_cnn = "${test_data_dir}/genomics/sarscov2/genome/cnn/reference.cnn"
kraken2 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
kraken2_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
@ -121,6 +123,7 @@ params {
genome_elfasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome.elfasta"
genome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome.fasta"
genome_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/genome.fasta.fai"
genome_strtablefile = "${test_data_dir}/genomics/homo_sapiens/genome/genome_strtablefile.zip"
genome_dict = "${test_data_dir}/genomics/homo_sapiens/genome/genome.dict"
genome_gff3 = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gff3"
genome_gtf = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gtf"
@ -146,6 +149,7 @@ params {
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 = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz"
genome_21_reference_cnn = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/reference_chr21.cnn"
dbsnp_146_hg38_elsites = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites"
dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
@ -263,6 +267,8 @@ params {
test_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
test2_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
test_paired_end_sorted_dragstrmodel = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt"
test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
test_pon_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
@ -324,6 +330,8 @@ params {
test_sv_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
test_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
test_flowcell = "${test_data_dir}/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz"
}
'pacbio' {
primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
@ -416,9 +424,6 @@ params {
'txt' {
hello = "${test_data_dir}/generic/txt/hello.txt"
}
'cnn' {
reference = "${test_data_dir}/generic/cnn/reference.cnn"
}
'cooler'{
test_pairix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"
test_pairix_pair_gz_px2 = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2"

18
tests/modules/bcftools/concat/main.nf
View file

@ -4,13 +4,25 @@ nextflow.enable.dsl = 2
include { BCFTOOLS_CONCAT } from '../../../../modules/bcftools/concat/main.nf'
workflow test_bcftools_concat {
workflow test_bcftools_concat_tbi {
input = [ [ id:'test3' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ]
file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) ]
]
BCFTOOLS_CONCAT ( input )
}
workflow test_bcftools_concat_no_tbi {
input = [ [ id:'test3' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
[]
]
BCFTOOLS_CONCAT ( input )
}

15
tests/modules/bcftools/concat/test.yml
View file

@ -1,8 +1,17 @@
- name: bcftools concat test_bcftools_concat
command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config
- name: bcftools concat test_bcftools_concat_tbi
command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config
tags:
- bcftools/concat
- bcftools
- bcftools/concat
files:
- path: output/bcftools/test3.vcf.gz
md5sum: 35c88bfaad20101062e98beb217d7137
- name: bcftools concat test_bcftools_concat_no_tbi
command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_no_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config
tags:
- bcftools
- bcftools/concat
files:
- path: output/bcftools/test3.vcf.gz
md5sum: 35c88bfaad20101062e98beb217d7137

35
tests/modules/bcftools/roh/main.nf Normal file
View file

@ -0,0 +1,35 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BCFTOOLS_ROH } from '../../../../modules/bcftools/roh/main.nf'
workflow test_bcftools_roh {
input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
af_file = [[],[]]
gen_map = []
regions = []
targets = []
samples = []
BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
}
workflow test_bcftools_roh_stub {
input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
af_file = [[],[]]
gen_map = []
regions = []
targets = []
samples = []
BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
}

5
tests/modules/bcftools/roh/nextflow.config Normal file
View file

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

17
tests/modules/bcftools/roh/test.yml Normal file
View file

@ -0,0 +1,17 @@
- name: "bcftools roh"
command: nextflow run ./tests/modules/bcftools/roh -entry test_bcftools_roh -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/roh/nextflow.config
tags:
- "bcftools"
- "bcftools/roh"
files:
- path: "output/bcftools/test.roh"
- path: "output/bcftools/versions.yml"
- name: "bcftools roh stub"
command: nextflow run ./tests/modules/bcftools/roh -entry test_bcftools_roh_stub -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/roh/nextflow.config
tags:
- "bcftools"
- "bcftools/roh"
files:
- path: "output/bcftools/test.roh"
- path: "output/bcftools/versions.yml"

58
tests/modules/cnvkit/batch/main.nf
View file

@ -5,8 +5,9 @@ nextflow.enable.dsl = 2
include { CNVKIT_BATCH as CNVKIT_HYBRID } from '../../../../modules/cnvkit/batch/main.nf'
include { CNVKIT_BATCH as CNVKIT_WGS } from '../../../../modules/cnvkit/batch/main.nf'
include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf'
include { CNVKIT_BATCH as CNVKIT_GERMLINE } from '../../../../modules/cnvkit/batch/main.nf'
workflow test_cnvkit_hybrid {
workflow test_cnvkit_hybrid_somatic {
input = [
[ id:'test' ], // meta map
@ -16,10 +17,10 @@ workflow test_cnvkit_hybrid {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
CNVKIT_HYBRID ( input, fasta, targets, [] )
CNVKIT_HYBRID ( input, fasta, [], targets, [] )
}
workflow test_cnvkit_wgs {
workflow test_cnvkit_wgs_somatic {
input = [
[ id:'test'], // meta map
@ -28,10 +29,10 @@ workflow test_cnvkit_wgs {
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
CNVKIT_WGS ( input, fasta, [], [] )
CNVKIT_WGS ( input, fasta, [], [], [] )
}
workflow test_cnvkit_cram {
workflow test_cnvkit_cram_wgs_somatic {
input = [
[ id:'test'], // meta map
@ -39,31 +40,60 @@ workflow test_cnvkit_cram {
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
CNVKIT_WGS ( input, fasta, [], [] )
CNVKIT_WGS ( input, fasta, fasta_fai, [], [] )
}
workflow test_cnvkit_tumoronly {
workflow test_cnvkit_tumoronly_hybrid_bam {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
[]
]
reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
CNVKIT_TUMORONLY ( input, [], [], reference )
CNVKIT_TUMORONLY ( input, [], [], [], reference )
}
workflow test_cnvkit_tumoronly_cram {
workflow test_cnvkit_tumoronly_hybrid_cram {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
CNVKIT_TUMORONLY ( input, fasta, [], reference )
CNVKIT_TUMORONLY ( input, fasta, [], [], reference )
}
workflow test_cnvkit_germline_hybrid_cram {
input = [
[ id:'test'], // meta map
[],
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
targets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
CNVKIT_GERMLINE ( input, fasta, fasta_fai, targets, [])
}
workflow test_cnvkit_germline_hybrid_bam {
input = [
[ id:'test'], // meta map
[],
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
targets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
CNVKIT_GERMLINE ( input, fasta, [], targets, [])
}

108
tests/modules/cnvkit/batch/test.yml
View file

@ -1,5 +1,5 @@
- name: cnvkit batch test_cnvkit_hybrid
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
- name: cnvkit batch test_cnvkit_hybrid_somatic
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid_somatic -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags:
- cnvkit
- cnvkit/batch
@ -26,8 +26,8 @@
- path: output/cnvkit/test.single_end.sorted.targetcoverage.cnn
md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7
- name: cnvkit batch test_cnvkit_wgs
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
- name: cnvkit batch test_cnvkit_wgs_somatic
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs_somatic -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags:
- cnvkit
- cnvkit/batch
@ -56,8 +56,8 @@
- path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
md5sum: 6ae6b3fce7299eedca6133d911c38fe1
- name: cnvkit batch test_cnvkit_cram
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
- name: cnvkit batch test_cnvkit_cram_wgs_somatic
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram_wgs_somatic -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags:
- cnvkit
- cnvkit/batch
@ -86,22 +86,98 @@
- path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
md5sum: 6ae6b3fce7299eedca6133d911c38fe1
- name: cnvkit batch test_cnvkit_tumoronly
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
- name: cnvkit batch test_cnvkit_tumoronly_hybrid_bam
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_bam -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags:
- cnvkit
- cnvkit/batch
files:
- path: output/cnvkit/reference.antitarget-tmp.bed
- path: output/cnvkit/reference.target-tmp.bed
md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
- path: output/cnvkit/reference_chr21.antitarget-tmp.bed
md5sum: 3d4d20f9f23b39970865d29ef239d20b
- path: output/cnvkit/reference_chr21.target-tmp.bed
md5sum: 657b25dbda8516624efa8cb2cf3716ca
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
md5sum: 067115082c4af4b64d58c0dc3a3642e4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
md5sum: f6adc75a0a86b7a921eca1b79a394cb0
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
md5sum: f7caeca04aba28b125ce26b511f42afb
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
md5sum: d9bdb71ce807051369577ee7f807a40c
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
md5sum: 2b56aac606ba6183d018b30ca58afcec
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
- name: cnvkit batch test_cnvkit_tumoronly_cram
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
- name: cnvkit batch test_cnvkit_tumoronly_hybrid_cram
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags:
- cnvkit
- cnvkit/batch
files:
- path: output/cnvkit/reference.antitarget-tmp.bed
- path: output/cnvkit/reference.target-tmp.bed
md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
- path: output/cnvkit/reference_chr21.antitarget-tmp.bed
md5sum: 3d4d20f9f23b39970865d29ef239d20b
- path: output/cnvkit/reference_chr21.target-tmp.bed
md5sum: 657b25dbda8516624efa8cb2cf3716ca
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
md5sum: 067115082c4af4b64d58c0dc3a3642e4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
md5sum: f6adc75a0a86b7a921eca1b79a394cb0
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
md5sum: f7caeca04aba28b125ce26b511f42afb
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
md5sum: d9bdb71ce807051369577ee7f807a40c
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
md5sum: 2b56aac606ba6183d018b30ca58afcec
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
- name: cnvkit batch test_cnvkit_germline_hybrid_cram
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags:
- cnvkit
- cnvkit/batch
files:
- path: output/cnvkit/multi_intervals.antitarget.bed
md5sum: 3d4d20f9f23b39970865d29ef239d20b
- path: output/cnvkit/multi_intervals.target.bed
md5sum: 86d30493bb2e619a93f4ebc2923d29f3
- path: output/cnvkit/reference.cnn
md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
md5sum: 067115082c4af4b64d58c0dc3a3642e4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
md5sum: 68b62b75cd91b2ffe5633686fb943490
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
md5sum: df196edd72613c59186f4d87df3dc4a4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
md5sum: 3b4fc0cc73be78f978cfe2422470753e
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
- name: cnvkit batch test_cnvkit_germline_hybrid_bam
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_bam -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags:
- cnvkit
- cnvkit/batch
files:
- path: output/cnvkit/multi_intervals.antitarget.bed
md5sum: 3d4d20f9f23b39970865d29ef239d20b
- path: output/cnvkit/multi_intervals.target.bed
md5sum: 86d30493bb2e619a93f4ebc2923d29f3
- path: output/cnvkit/reference.cnn
md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
md5sum: 067115082c4af4b64d58c0dc3a3642e4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
md5sum: 68b62b75cd91b2ffe5633686fb943490
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
md5sum: df196edd72613c59186f4d87df3dc4a4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
md5sum: 3b4fc0cc73be78f978cfe2422470753e
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
md5sum: b4a49faf170e436ec32dcc21ccc3ce8f

2
tests/modules/cnvkit/reference/test.yml
View file

@ -4,5 +4,5 @@
- cnvkit/reference
- cnvkit
files:
- path: output/cnvkit/reference.cnn
- path: output/cnvkit/multi_intervals.reference.cnn
md5sum: 7c4a7902f5ab101b1f9d6038d331b3d9

18
tests/modules/deeptools/bamcoverage/main.nf
View file

@ -12,7 +12,7 @@ workflow test_deeptools_bamcoverage_bam {
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
]
DEEPTOOLS_BAMCOVERAGE ( input )
DEEPTOOLS_BAMCOVERAGE ( input, [], [] )
}
workflow test_deeptools_bamcoverage_cram {
@ -22,6 +22,20 @@ workflow test_deeptools_bamcoverage_cram {
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
DEEPTOOLS_BAMCOVERAGE ( input )
DEEPTOOLS_BAMCOVERAGE ( input, fasta, fasta_fai)
}
workflow test_deeptools_bamcoverage_cram_no_fasta_fai {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
DEEPTOOLS_BAMCOVERAGE ( input, fasta, [])
}

21
tests/modules/deeptools/bamcoverage/test.yml
View file

@ -1,21 +1,26 @@
- name: deeptools bamcoverage test_deeptools_bamcoverage_bam
command: nextflow run tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_bam -c tests/config/nextflow.config
command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_bam -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/bamcoverage/nextflow.config
tags:
- deeptools
- deeptools/bamcoverage
- deeptools
files:
- path: output/deeptools/test.bigWig
md5sum: 95fe9383a9e6c02aea6b785cf074274f
- path: output/deeptools/versions.yml
md5sum: 68c94e73b7a8c0935578bad61fea54c1
- name: deeptools bamcoverage test_deeptools_bamcoverage_cram
command: nextflow run tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram -c tests/config/nextflow.config
command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/bamcoverage/nextflow.config
tags:
- deeptools
- deeptools/bamcoverage
- deeptools
files:
- path: output/deeptools/test.bigWig
md5sum: 95fe9383a9e6c02aea6b785cf074274f
- name: deeptools bamcoverage test_deeptools_bamcoverage_cram_no_fasta_fai
command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram_no_fasta_fai -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/bamcoverage/nextflow.config
tags:
- deeptools/bamcoverage
- deeptools
files:
- path: output/deeptools/test.bigWig
md5sum: 95fe9383a9e6c02aea6b785cf074274f
- path: output/deeptools/versions.yml
md5sum: 665bbd2979c49bf3974a24bd44a88e94

15
tests/modules/ensemblvep/main.nf
View file

@ -4,11 +4,22 @@ nextflow.enable.dsl = 2
include { ENSEMBLVEP } from '../../../modules/ensemblvep/main.nf'
workflow test_ensemblvep {
workflow test_ensemblvep_fasta {
input = [
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
]
ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], [] )
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] )
}
workflow test_ensemblvep_no_fasta {
input = [
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
]
ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], [], [] )
}

12
tests/modules/ensemblvep/test.yml
View file

@ -1,5 +1,13 @@
- name: ensemblvep test_ensemblvep
command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
- name: ensemblvep test_ensemblvep_fasta
command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
tags:
- ensemblvep
files:
- path: output/ensemblvep/test.ann.vcf
- path: output/ensemblvep/test.summary.html
- name: ensemblvep test_ensemblvep_no_fasta
command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_no_fasta -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
tags:
- ensemblvep
files:

3
tests/modules/filtlong/nextflow.config
View file

@ -2,4 +2,7 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
ext.args = "--min_length 10"
ext.prefix = "test_lr"
}

15
tests/modules/filtlong/test.yml
View file

@ -3,21 +3,24 @@
tags:
- filtlong
files:
- path: output/filtlong/test_lr_filtlong.fastq.gz
md5sum: 7029066c27ac6f5ef18d660d5741979a
- path: output/filtlong/test_lr.fastq.gz
contains:
- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
- name: filtlong test_filtlong_illumina_se
command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
tags:
- filtlong
files:
- path: output/filtlong/test_lr_filtlong.fastq.gz
md5sum: 7029066c27ac6f5ef18d660d5741979a
- path: output/filtlong/test_lr.fastq.gz
contains:
- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
- name: filtlong test_filtlong_illumina_pe
command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
tags:
- filtlong
files:
- path: output/filtlong/test_lr_filtlong.fastq.gz
md5sum: 7029066c27ac6f5ef18d660d5741979a
- path: output/filtlong/test_lr.fastq.gz
contains:
- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"

29
tests/modules/gamma/gamma/main.nf Normal file
View file

@ -0,0 +1,29 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GAMMA_GAMMA } from '../../../../modules/gamma/gamma/main.nf'
workflow test_unzip {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true),
]
db = [ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/ResGANNCBI_20210507_srst2.fasta", checkIfExists: true), ]
GAMMA_GAMMA ( input, db )
}
workflow test_gamma {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
db = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
GAMMA_GAMMA ( input, db )
}

0
tests/modules/gamma/nextflow.config → tests/modules/gamma/gamma/nextflow.config
View file

29
tests/modules/gamma/gamma/test.yml Normal file
View file

@ -0,0 +1,29 @@
- name: gamma gamma test_unzip
command: nextflow run tests/modules/gamma/gamma -entry test_unzip -c tests/config/nextflow.config
tags:
- gamma/gamma
- gamma
files:
- path: output/gamma/test.fasta
md5sum: 5b3b831d863fffaa3410a9ee7bfa12ce
- path: output/gamma/test.gamma
md5sum: 46165a89e10b7315d3a9b0aa6c561626
- path: output/gamma/test.psl
md5sum: f489ce4602ddbcb692d5781ee3fbf449
- path: output/gamma/versions.yml
md5sum: 8baafec7b3b87f788f69e30d317c9722
- name: gamma gamma test_gamma
command: nextflow run tests/modules/gamma/gamma -entry test_gamma -c tests/config/nextflow.config
tags:
- gamma/gamma
- gamma
files:
- path: output/gamma/test.fasta
md5sum: df37b48466181311e0a679f3c5878484
- path: output/gamma/test.gamma
md5sum: 3256708fa517a65ed01d99e0e3c762ae
- path: output/gamma/test.psl
md5sum: 162a2757ed3b167ae1e0cdb24213f940
- path: output/gamma/versions.yml
md5sum: b75c2871d8cac2f8ac67c0fbd22babd6

17
tests/modules/gamma/main.nf
View file

@ -1,17 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GAMMA } from '../../../modules/gamma/main.nf'
workflow test_gamma {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
db = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
GAMMA ( input, db )
}

13
tests/modules/gamma/test.yml
View file

@ -1,13 +0,0 @@
- name: gamma test_gamma
command: nextflow run tests/modules/gamma -entry test_gamma -c tests/config/nextflow.config
tags:
- gamma
files:
- path: output/gamma/test.fasta
md5sum: df37b48466181311e0a679f3c5878484
- path: output/gamma/test.gamma
md5sum: 3256708fa517a65ed01d99e0e3c762ae
- path: output/gamma/test.psl
md5sum: 162a2757ed3b167ae1e0cdb24213f940
- path: output/gamma/versions.yml
md5sum: 3fefb5b46c94993362243c5f9a472057

33
tests/modules/gatk/indelrealigner/main.nf Normal file
View file

@ -0,0 +1,33 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/gatk/realignertargetcreator/main.nf'
include { GATK_INDELREALIGNER } from '../../../../modules/gatk/indelrealigner/main.nf'
workflow test_gatk_indelrealigner {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
input_realignertargetcreator = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
]
GATK_REALIGNERTARGETCREATOR ( input_realignertargetcreator, fasta, fai, dict, [] )
ch_intervals = GATK_REALIGNERTARGETCREATOR.out.intervals
ch_bams_indelrealigner = Channel.of([ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
])
ch_input_indelrealigner = ch_bams_indelrealigner.mix(ch_intervals).groupTuple(by: 0).map{ [it[0], it[1][0], it[2], it[1][1] ] }.dump(tag: "input")
GATK_INDELREALIGNER ( ch_input_indelrealigner, fasta, fai, dict, [] )
}

6
tests/modules/gatk/indelrealigner/nextflow.config Normal file
View file

@ -0,0 +1,6 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
ext.prefix = { "${meta.id}.realigned" }
}

12
tests/modules/gatk/indelrealigner/test.yml Normal file
View file

@ -0,0 +1,12 @@
- name: gatk indelrealigner test_gatk_indelrealigner
command: nextflow run ./tests/modules/gatk/indelrealigner -entry test_gatk_indelrealigner -c ./tests/config/nextflow.config -c ./tests/modules/gatk/indelrealigner/nextflow.config
tags:
- gatk/indelrealigner
- gatk
files:
- path: output/gatk/test.realigned.bai
md5sum: 85a67df8827fe426e7f3a458134c0551
- path: output/gatk/test.realigned.bam
md5sum: ea1df6f7fcafc408fae4dc1574813d8a
- path: output/gatk/test.realigned.intervals
md5sum: 7aa7a1b235a510e6591e262382086bf8

18
tests/modules/gatk/realignertargetcreator/main.nf Normal file
View file

@ -0,0 +1,18 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/gatk/realignertargetcreator/main.nf'
workflow test_gatk_realignertargetcreator {
input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK_REALIGNERTARGETCREATOR ( input, fasta, fai, dict, [] )
}

5
tests/modules/gatk/realignertargetcreator/nextflow.config Normal file
View file

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

8
tests/modules/gatk/realignertargetcreator/test.yml Normal file
View file

@ -0,0 +1,8 @@
- name: gatk realignertargetcreator test_gatk_realignertargetcreator
command: nextflow run ./tests/modules/gatk/realignertargetcreator -entry test_gatk_realignertargetcreator -c ./tests/config/nextflow.config -c ./tests/modules/gatk/realignertargetcreator/nextflow.config
tags:
- gatk
- gatk/realignertargetcreator
files:
- path: output/gatk/test.intervals
md5sum: 7aa7a1b235a510e6591e262382086bf8

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