mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 02:58:17 +00:00
Merge branch 'master' into r-ampir
This commit is contained in:
James A. Fellows Yates
GitHub
commit
c9db677a45
103 changed files with 2273 additions and 277 deletions
|
|
@ -9,7 +9,7 @@ process BCFTOOLS_ROH {
|
|||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi)
|
||||
path af_file
|
||||
tuple path(af_file), path(af_file_tbi)
|
||||
path genetic_map
|
||||
path regions_file
|
||||
path samples_file
|
||||
|
|
|
|||
|
|
@ -23,6 +23,9 @@ input:
|
|||
- 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."
|
||||
|
|
|
|||
|
|
@ -10,6 +10,7 @@ process CNVKIT_BATCH {
|
|||
input:
|
||||
tuple val(meta), path(tumor), path(normal)
|
||||
path fasta
|
||||
path fasta_fai
|
||||
path targets
|
||||
path reference
|
||||
|
||||
|
|
@ -28,48 +29,167 @@ 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" : ""
|
||||
|
||||
"""
|
||||
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
|
||||
// somatic_mode cram_input
|
||||
if (tumor_cram && normal_cram){
|
||||
"""
|
||||
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
|
||||
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 \\
|
||||
$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
|
||||
"""
|
||||
}
|
||||
// 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
|
||||
"""
|
||||
}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -29,6 +29,10 @@ input:
|
|||
type: file
|
||||
description: |
|
||||
Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)
|
||||
- fasta_fai:
|
||||
type: file
|
||||
description: |
|
||||
Input reference genome fasta index (optional, but recommended for cram_input)
|
||||
- targetfile:
|
||||
type: file
|
||||
description: |
|
||||
|
|
|
|||
|
|
@ -2,13 +2,15 @@ process DEEPTOOLS_BAMCOVERAGE {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0':
|
||||
'quay.io/biocontainers/deeptools:3.5.1--py_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0':
|
||||
'quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index)
|
||||
path(fasta)
|
||||
path(fasta_fai)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bigWig") , emit: bigwig, optional: true
|
||||
|
|
@ -22,16 +24,44 @@ process DEEPTOOLS_BAMCOVERAGE {
|
|||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}.bigWig"
|
||||
|
||||
"""
|
||||
bamCoverage \\
|
||||
--bam $input \\
|
||||
$args \\
|
||||
--numberOfProcessors ${task.cpus} \\
|
||||
--outFileName ${prefix}
|
||||
// cram_input is currently not working with deeptools
|
||||
// therefore it's required to convert cram to bam first
|
||||
def is_cram = input.Extension == "cram" ? true : false
|
||||
def input_out = is_cram ? input.BaseName + ".bam" : "${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_out \\
|
||||
$args \\
|
||||
--numberOfProcessors ${task.cpus} \\
|
||||
--outFileName ${prefix}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -25,6 +25,14 @@ input:
|
|||
type: file
|
||||
description: BAM/CRAM index file
|
||||
pattern: "*.{bai,crai}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Reference file the CRAM file was created with (required with CRAM input)
|
||||
pattern: "*.{fasta,fa}"
|
||||
- fasta_fai:
|
||||
type: file
|
||||
description: Index of the reference file (optional, but recommended)
|
||||
pattern: "*.{fai}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
|
|
@ -47,3 +55,4 @@ output:
|
|||
|
||||
authors:
|
||||
- "@FriederikeHanssen"
|
||||
- "@SusiJo"
|
||||
|
|
|
|||
|
|
@ -11,8 +11,8 @@ RUN conda env create -f /environment.yml && conda clean -a
|
|||
# Setup default ARG variables
|
||||
ARG GENOME=GRCh38
|
||||
ARG SPECIES=homo_sapiens
|
||||
ARG VEP_VERSION=104
|
||||
ARG VEP_TAG=104.3
|
||||
ARG VEP_VERSION=105
|
||||
ARG VEP_TAG=105.0
|
||||
|
||||
# Add conda installation dir to PATH (instead of doing 'conda activate')
|
||||
ENV PATH /opt/conda/envs/nf-core-vep-${VEP_TAG}/bin:$PATH
|
||||
|
|
|
|||
|
|
@ -20,9 +20,9 @@ build_push() {
|
|||
docker push nfcore/vep:${VEP_TAG}.${GENOME}
|
||||
}
|
||||
|
||||
build_push "GRCh37" "homo_sapiens" "104" "104.3"
|
||||
build_push "GRCh38" "homo_sapiens" "104" "104.3"
|
||||
build_push "GRCm38" "mus_musculus" "102" "104.3"
|
||||
build_push "GRCm39" "mus_musculus" "104" "104.3"
|
||||
build_push "CanFam3.1" "canis_lupus_familiaris" "104" "104.3"
|
||||
build_push "WBcel235" "caenorhabditis_elegans" "104" "104.3"
|
||||
build_push "GRCh37" "homo_sapiens" "105" "105.0"
|
||||
build_push "GRCh38" "homo_sapiens" "105" "105.0"
|
||||
build_push "GRCm38" "mus_musculus" "102" "105.0"
|
||||
build_push "GRCm39" "mus_musculus" "105" "105.0"
|
||||
build_push "CanFam3.1" "canis_lupus_familiaris" "104" "105.0"
|
||||
build_push "WBcel235" "caenorhabditis_elegans" "105" "105.0"
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
# You can use this file to create a conda environment for this module:
|
||||
# conda env create -f environment.yml
|
||||
name: nf-core-vep-104.3
|
||||
name: nf-core-vep-105.0
|
||||
channels:
|
||||
- conda-forge
|
||||
- bioconda
|
||||
- defaults
|
||||
|
||||
dependencies:
|
||||
- bioconda::ensembl-vep=104.3
|
||||
- bioconda::ensembl-vep=105.0
|
||||
|
|
|
|||
|
|
@ -13,6 +13,7 @@ process ENSEMBLVEP {
|
|||
val species
|
||||
val cache_version
|
||||
path cache
|
||||
path fasta
|
||||
path extra_files
|
||||
|
||||
output:
|
||||
|
|
@ -27,6 +28,8 @@ process ENSEMBLVEP {
|
|||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${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 $species \\
|
||||
--cache \\
|
||||
|
|
|
|||
|
|
@ -36,6 +36,11 @@ input:
|
|||
type: file
|
||||
description: |
|
||||
path to VEP cache (optional)
|
||||
- fasta:
|
||||
type: file
|
||||
description: |
|
||||
reference FASTA file (optional)
|
||||
pattern: "*.{fasta,fa}"
|
||||
- extra_files:
|
||||
type: tuple
|
||||
description: |
|
||||
|
|
|
|||
54
modules/gatk/indelrealigner/main.nf
Normal file
54
modules/gatk/indelrealigner/main.nf
Normal file
|
|
@ -0,0 +1,54 @@
|
|||
process GATK_INDELREALIGNER {
|
||||
tag "$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
71
modules/gatk/indelrealigner/meta.yml
Normal 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
53
modules/gatk/realignertargetcreator/main.nf
Normal file
|
|
@ -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
64
modules/gatk/realignertargetcreator/meta.yml
Normal file
|
|
@ -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
63
modules/gatk/unifiedgenotyper/main.nf
Normal file
|
|
@ -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
73
modules/gatk/unifiedgenotyper/meta.yml
Normal file
|
|
@ -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"
|
||||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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
51
modules/gatk4/calibratedragstrmodel/main.nf
Normal file
|
|
@ -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
74
modules/gatk4/calibratedragstrmodel/meta.yml
Normal file
|
|
@ -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
53
modules/gatk4/composestrtablefile/main.nf
Normal file
|
|
@ -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
43
modules/gatk4/composestrtablefile/meta.yml
Normal file
|
|
@ -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"
|
||||
|
|
@ -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 . \\
|
||||
$args
|
||||
|
||||
|
|
|
|||
|
|
@ -32,6 +32,10 @@ input:
|
|||
- intervals:
|
||||
type: file
|
||||
description: Bed file with the genomic regions included in the library (optional)
|
||||
- dragstr_model:
|
||||
type: file
|
||||
description: Text file containing the DragSTR model of the used BAM/CRAM file (optional)
|
||||
pattern: "*.txt"
|
||||
- fasta:
|
||||
type: file
|
||||
description: The reference fasta file
|
||||
|
|
|
|||
|
|
@ -2,10 +2,8 @@ process GATK4_MARKDUPLICATES_SPARK {
|
|||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'broadinstitute/gatk:4.2.3.0' }"
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null)
|
||||
container 'broadinstitute/gatk:4.2.6.1'
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
@ -14,8 +12,9 @@ process GATK4_MARKDUPLICATES_SPARK {
|
|||
path dict
|
||||
|
||||
output:
|
||||
tuple val(meta), path("${prefix}"), emit: output
|
||||
path "versions.yml" , emit: versions
|
||||
tuple val(meta), path("${prefix}"), emit: output
|
||||
tuple val(meta), path("*.metrics"), emit: metrics, optional: true
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
|
@ -25,6 +24,7 @@ process GATK4_MARKDUPLICATES_SPARK {
|
|||
prefix = task.ext.prefix ?: "${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
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -58,3 +58,4 @@ authors:
|
|||
- "@ajodeh-juma"
|
||||
- "@FriederikeHanssen"
|
||||
- "@maxulysse"
|
||||
- "@SusiJo"
|
||||
|
|
|
|||
52
modules/gatk4/reblockgvcf/main.nf
Normal file
52
modules/gatk4/reblockgvcf/main.nf
Normal file
|
|
@ -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
74
modules/gatk4/reblockgvcf/meta.yml
Normal file
|
|
@ -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"
|
||||
|
|
@ -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}":
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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
51
modules/rhocall/annotate/main.nf
Normal 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
54
modules/rhocall/annotate/meta.yml
Normal file
|
|
@ -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
55
modules/snippy/run/main.nf
Normal 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
110
modules/snippy/run/meta.yml
Normal 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"
|
||||
|
|
@ -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
|
||||
"${task.process}":
|
||||
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
|
||||
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -19,7 +19,7 @@ input:
|
|||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
- input:
|
||||
type: file
|
||||
description: BAM/CRAM file
|
||||
pattern: "*.{bam,cram}"
|
||||
|
|
|
|||
|
|
@ -2,21 +2,20 @@ process TIDDIT_SV {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0' :
|
||||
'quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/tiddit:3.0.0--py39h59fae87_1' :
|
||||
'quay.io/biocontainers/tiddit:3.0.0--py39h59fae87_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
tuple val(meta), path(input), path(input_index)
|
||||
path fasta
|
||||
path fai
|
||||
path bwa_index
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.vcf") , emit: vcf
|
||||
tuple val(meta), path("*.ploidy.tab") , emit: ploidy
|
||||
tuple val(meta), path("*.signals.tab"), emit: signals
|
||||
path "versions.yml" , emit: versions
|
||||
tuple val(meta), path("*.vcf") , emit: vcf
|
||||
tuple val(meta), path("*.ploidies.tab"), emit: ploidy
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
|
@ -24,18 +23,19 @@ process TIDDIT_SV {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${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
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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}":
|
||||
|
|
|
|||
|
|
@ -719,6 +719,18 @@ 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/**
|
||||
- tests/modules/gatk4/applybqsr/**
|
||||
|
|
@ -747,6 +759,10 @@ 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/**
|
||||
|
|
@ -755,6 +771,10 @@ 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/**
|
||||
|
|
@ -843,6 +863,10 @@ 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/**
|
||||
|
|
@ -1639,6 +1663,10 @@ rgi/main:
|
|||
- modules/rgi/main/**
|
||||
- tests/modules/rgi/main/**
|
||||
|
||||
rhocall/annotate:
|
||||
- modules/rhocall/annotate/**
|
||||
- tests/modules/rhocall/annotate/**
|
||||
|
||||
rmarkdownnotebook:
|
||||
- modules/rmarkdownnotebook/**
|
||||
- tests/modules/rmarkdownnotebook/**
|
||||
|
|
@ -1855,6 +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/**
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
|
@ -262,6 +266,8 @@ 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 = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
|
||||
|
||||
|
|
@ -323,6 +329,8 @@ params {
|
|||
test_sv_vcf = "${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 = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
|
||||
|
|
@ -415,9 +423,6 @@ params {
|
|||
'txt' {
|
||||
hello = "${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"
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@ workflow test_bcftools_roh {
|
|||
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 = []
|
||||
af_file = [[],[]]
|
||||
gen_map = []
|
||||
regions = []
|
||||
targets = []
|
||||
|
|
@ -25,7 +25,7 @@ workflow test_bcftools_roh_stub {
|
|||
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 = []
|
||||
af_file = [[],[]]
|
||||
gen_map = []
|
||||
regions = []
|
||||
targets = []
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
@ -28,42 +29,71 @@ 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
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
|
||||
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 = 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, [])
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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, [])
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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", [], [], [] )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
|
|||
33
tests/modules/gatk/indelrealigner/main.nf
Normal file
33
tests/modules/gatk/indelrealigner/main.nf
Normal 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
6
tests/modules/gatk/indelrealigner/nextflow.config
Normal 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
12
tests/modules/gatk/indelrealigner/test.yml
Normal 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
18
tests/modules/gatk/realignertargetcreator/main.nf
Normal 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, [] )
|
||||
}
|
||||
|
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
8
tests/modules/gatk/realignertargetcreator/test.yml
Normal file
8
tests/modules/gatk/realignertargetcreator/test.yml
Normal 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
|
||||
18
tests/modules/gatk/unifiedgenotyper/main.nf
Normal file
18
tests/modules/gatk/unifiedgenotyper/main.nf
Normal file
|
|
@ -0,0 +1,18 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { GATK_UNIFIEDGENOTYPER } from '../../../../modules/gatk/unifiedgenotyper/main.nf'
|
||||
|
||||
workflow test_gatk_unifiedgenotyper {
|
||||
|
||||
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_UNIFIEDGENOTYPER ( input, fasta, fai, dict, [], [], [], [])
|
||||
}
|
||||
5
tests/modules/gatk/unifiedgenotyper/nextflow.config
Normal file
5
tests/modules/gatk/unifiedgenotyper/nextflow.config
Normal file
|
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
9
tests/modules/gatk/unifiedgenotyper/test.yml
Normal file
9
tests/modules/gatk/unifiedgenotyper/test.yml
Normal file
|
|
@ -0,0 +1,9 @@
|
|||
- name: gatk unifiedgenotyper test_gatk_unifiedgenotyper
|
||||
command: nextflow run ./tests/modules/gatk/unifiedgenotyper -entry test_gatk_unifiedgenotyper -c ./tests/config/nextflow.config -c ./tests/modules/gatk/unifiedgenotyper/nextflow.config
|
||||
tags:
|
||||
- gatk
|
||||
- gatk/unifiedgenotyper
|
||||
files:
|
||||
- path: output/gatk/test.vcf.gz
|
||||
contains:
|
||||
- "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test"
|
||||
|
|
@ -15,7 +15,6 @@
|
|||
- gatk4/applybqsrspark
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 2ca2446f0125890280056fd7da822732
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 applybqsr test_gatk4_applybqsr_spark_cram
|
||||
|
|
|
|||
66
tests/modules/gatk4/calibratedragstrmodel/main.nf
Normal file
66
tests/modules/gatk4/calibratedragstrmodel/main.nf
Normal file
|
|
@ -0,0 +1,66 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { GATK4_CALIBRATEDRAGSTRMODEL } from '../../../../modules/gatk4/calibratedragstrmodel/main.nf'
|
||||
|
||||
workflow test_gatk4_calibratedragstrmodel_bam {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], 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)
|
||||
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
|
||||
|
||||
GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
|
||||
}
|
||||
|
||||
workflow test_gatk4_calibratedragstrmodel_cram {
|
||||
|
||||
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)
|
||||
|
||||
fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
|
||||
|
||||
GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
|
||||
}
|
||||
|
||||
workflow test_gatk4_calibratedragstrmodel_beds {
|
||||
|
||||
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),
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_bed'], 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)
|
||||
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
|
||||
|
||||
GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
26
tests/modules/gatk4/calibratedragstrmodel/test.yml
Normal file
26
tests/modules/gatk4/calibratedragstrmodel/test.yml
Normal file
|
|
@ -0,0 +1,26 @@
|
|||
- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_bam
|
||||
command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_bam -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/calibratedragstrmodel
|
||||
files:
|
||||
- path: output/gatk4/test.txt
|
||||
md5sum: e16fa32906c74bb18b93e98a86718ff1
|
||||
|
||||
- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_cram
|
||||
command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_cram -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/calibratedragstrmodel
|
||||
files:
|
||||
- path: output/gatk4/test.txt
|
||||
md5sum: 81c7bf338886cb4d5c2cc07fc56afe44
|
||||
|
||||
- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_beds
|
||||
command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_beds -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/calibratedragstrmodel
|
||||
files:
|
||||
- path: output/gatk4/test.txt
|
||||
md5sum: cb6a9acdee042302b54fd1f59b5f54ee
|
||||
16
tests/modules/gatk4/composestrtablefile/main.nf
Normal file
16
tests/modules/gatk4/composestrtablefile/main.nf
Normal file
|
|
@ -0,0 +1,16 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { GATK4_COMPOSESTRTABLEFILE } from '../../../../modules/gatk4/composestrtablefile/main.nf'
|
||||
|
||||
workflow test_gatk4_composestrtablefile {
|
||||
|
||||
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)
|
||||
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
GATK4_COMPOSESTRTABLEFILE ( fasta, fasta_fai, dict )
|
||||
}
|
||||
5
tests/modules/gatk4/composestrtablefile/nextflow.config
Normal file
5
tests/modules/gatk4/composestrtablefile/nextflow.config
Normal file
|
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
7
tests/modules/gatk4/composestrtablefile/test.yml
Normal file
7
tests/modules/gatk4/composestrtablefile/test.yml
Normal file
|
|
@ -0,0 +1,7 @@
|
|||
- name: gatk4 composestrtablefile test_gatk4_composestrtablefile
|
||||
command: nextflow run ./tests/modules/gatk4/composestrtablefile -entry test_gatk4_composestrtablefile -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/composestrtablefile/nextflow.config
|
||||
tags:
|
||||
- gatk4/composestrtablefile
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/genome.zip
|
||||
|
|
@ -8,6 +8,7 @@ workflow test_gatk4_haplotypecaller {
|
|||
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)
|
||||
|
|
@ -21,6 +22,7 @@ workflow test_gatk4_haplotypecaller_cram {
|
|||
input = [ [ id:'test' ], // 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)
|
||||
|
|
@ -34,7 +36,8 @@ workflow test_gatk4_haplotypecaller_intervals_dbsnp {
|
|||
input = [ [ id:'test' ], // 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),
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
|
||||
[]
|
||||
]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
|
@ -45,3 +48,20 @@ workflow test_gatk4_haplotypecaller_intervals_dbsnp {
|
|||
|
||||
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
|
||||
}
|
||||
|
||||
workflow test_gatk4_haplotypecaller_dragstr_model {
|
||||
input = [ [ id:'test' ], // 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),
|
||||
[],
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_dragstrmodel'], checkIfExists: true)
|
||||
]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
sites = []
|
||||
sites_tbi = []
|
||||
|
||||
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -6,7 +6,6 @@
|
|||
files:
|
||||
- path: output/gatk4/test.vcf.gz
|
||||
- path: output/gatk4/test.vcf.gz.tbi
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_cram
|
||||
command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_cram -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
|
||||
|
|
@ -16,7 +15,6 @@
|
|||
files:
|
||||
- path: output/gatk4/test.vcf.gz
|
||||
- path: output/gatk4/test.vcf.gz.tbi
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_intervals_dbsnp
|
||||
command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_intervals_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
|
||||
|
|
@ -26,4 +24,12 @@
|
|||
files:
|
||||
- path: output/gatk4/test.vcf.gz
|
||||
- path: output/gatk4/test.vcf.gz.tbi
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_dragstr_model
|
||||
command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_dragstr_model -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
|
||||
tags:
|
||||
- gatk4/haplotypecaller
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.vcf.gz
|
||||
- path: output/gatk4/test.vcf.gz.tbi
|
||||
|
|
|
|||
|
|
@ -3,26 +3,55 @@
|
|||
nextflow.enable.dsl = 2
|
||||
|
||||
include { GATK4_MARKDUPLICATES_SPARK } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
|
||||
include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_CRAM } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
|
||||
include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_METRICS } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
|
||||
|
||||
workflow test_gatk4_markduplicates_spark {
|
||||
input = [ [ id:'test', single_end:false ], // 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'], checkIfExists: true)
|
||||
]
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||||
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)
|
||||
|
||||
GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
|
||||
}
|
||||
|
||||
// chr 22
|
||||
workflow test_gatk4_markduplicates_spark_multiple_bams {
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
|
||||
] ]
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
|
||||
}
|
||||
|
||||
// chr 22
|
||||
workflow test_gatk4_markduplicates_spark_multiple_bams_cram_out {
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
|
||||
] ]
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
GATK4_MARKDUPLICATES_SPARK_CRAM ( input, fasta, fai, dict )
|
||||
}
|
||||
|
||||
// chr 22
|
||||
workflow test_gatk4_markduplicates_spark_multiple_bams_metrics {
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
|
||||
] ]
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
GATK4_MARKDUPLICATES_SPARK_METRICS ( input, fasta, fai, dict )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,4 +2,18 @@ process {
|
|||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
withName: GATK4_MARKDUPLICATES_SPARK {
|
||||
ext.prefix = { "${meta.id}.bam" }
|
||||
}
|
||||
withName: GATK4_MARKDUPLICATES_SPARK_CRAM {
|
||||
ext.prefix = { "${meta.id}.cram" }
|
||||
}
|
||||
withName: GATK4_MARKDUPLICATES_SPARK_METRICS {
|
||||
ext.args = '--metrics-file test.metrics'
|
||||
ext.prefix = { "${meta.id}.bam" }
|
||||
}
|
||||
|
||||
}
|
||||
// override tests/config/nextflow.config
|
||||
docker.userEmulation = false
|
||||
|
||||
|
|
|
|||
|
|
@ -1,25 +1,41 @@
|
|||
- name: gatk4 markduplicates test_gatk4_markduplicates_spark
|
||||
command: nextflow run tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
|
||||
- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark
|
||||
command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/markduplicatesspark
|
||||
files:
|
||||
- path: output/gatk4/test.bai
|
||||
md5sum: e9c125e82553209933883b4fe2b8d7c2
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 2efd50b2e6b7fd9bdf242cd9e266cfa9
|
||||
- path: output/gatk4/test.metrics
|
||||
md5sum: dc1a09ac6371aab7c50d1a554baa06d3
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 markduplicates test_gatk4_markduplicates_spark_multiple_bams
|
||||
command: nextflow run tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
|
||||
- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams
|
||||
command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/markduplicatesspark
|
||||
files:
|
||||
- path: output/gatk4/test.bai
|
||||
md5sum: bad71df9c876e72a5bc0a3e0fd755f92
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 8187febc6108ffef7f907e89b9c091a4
|
||||
- path: output/gatk4/test.metrics
|
||||
md5sum: 898cb0a6616897d8ada90bab53bf0837
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams_cram_out
|
||||
command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams_cram_out -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/markduplicatesspark
|
||||
files:
|
||||
- path: output/gatk4/test.cram
|
||||
md5sum: 2271016de5e4199736598f39d12d7587
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams_metrics
|
||||
command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams_metrics -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/markduplicatesspark
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 898cb0a6616897d8ada90bab53bf0837
|
||||
- path: output/gatk4/test.metrics
|
||||
contains: ["## METRICS CLASS", "org.broadinstitute.hellbender.utils.read.markduplicates.GATKDuplicationMetrics"]
|
||||
- path: output/gatk4/versions.yml
|
||||
|
|
|
|||
55
tests/modules/gatk4/reblockgvcf/main.nf
Normal file
55
tests/modules/gatk4/reblockgvcf/main.nf
Normal file
|
|
@ -0,0 +1,55 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { GATK4_REBLOCKGVCF } from '../../../../modules/gatk4/reblockgvcf/main.nf'
|
||||
|
||||
workflow test_gatk4_reblockgvcf {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // 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),
|
||||
[]
|
||||
]
|
||||
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fasta_index = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
GATK4_REBLOCKGVCF ( input, fasta, fasta_index, dict, [], [] )
|
||||
}
|
||||
|
||||
workflow test_gatk4_reblockgvcf_intervals {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // 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),
|
||||
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
|
||||
]
|
||||
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fasta_index = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
GATK4_REBLOCKGVCF ( input, fasta, fasta_index, dict, [], [] )
|
||||
}
|
||||
|
||||
workflow test_gatk4_reblockgvcf_dbsnp {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true),
|
||||
[]
|
||||
]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fasta_index = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
|
||||
dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
|
||||
|
||||
GATK4_REBLOCKGVCF ( input, fasta, fasta_index, dict, dbsnp, dbsnp_tbi )
|
||||
}
|
||||
5
tests/modules/gatk4/reblockgvcf/nextflow.config
Normal file
5
tests/modules/gatk4/reblockgvcf/nextflow.config
Normal file
|
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
26
tests/modules/gatk4/reblockgvcf/test.yml
Normal file
26
tests/modules/gatk4/reblockgvcf/test.yml
Normal file
|
|
@ -0,0 +1,26 @@
|
|||
- name: gatk4 reblockgvcf test_gatk4_reblockgvcf
|
||||
command: nextflow run ./tests/modules/gatk4/reblockgvcf -entry test_gatk4_reblockgvcf -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/reblockgvcf/nextflow.config
|
||||
tags:
|
||||
- gatk4/reblockgvcf
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.rb.g.vcf.gz
|
||||
- path: output/gatk4/test.rb.g.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 reblockgvcf test_gatk4_reblockgvcf_intervals
|
||||
command: nextflow run ./tests/modules/gatk4/reblockgvcf -entry test_gatk4_reblockgvcf_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/reblockgvcf/nextflow.config
|
||||
tags:
|
||||
- gatk4/reblockgvcf
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.rb.g.vcf.gz
|
||||
- path: output/gatk4/test.rb.g.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 reblockgvcf test_gatk4_reblockgvcf_dbsnp
|
||||
command: nextflow run ./tests/modules/gatk4/reblockgvcf -entry test_gatk4_reblockgvcf_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/reblockgvcf/nextflow.config
|
||||
tags:
|
||||
- gatk4/reblockgvcf
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.rb.g.vcf.gz
|
||||
- path: output/gatk4/test.rb.g.vcf.gz.tbi
|
||||
|
|
@ -2,15 +2,32 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { FASTQC } from '../../../modules/fastqc/main.nf'
|
||||
include { MULTIQC } from '../../../modules/multiqc/main.nf'
|
||||
include { FASTQC } from '../../../modules/fastqc/main.nf'
|
||||
include { FASTQC as FASTQC2 } from '../../../modules/fastqc/main.nf'
|
||||
include { MULTIQC } from '../../../modules/multiqc/main.nf'
|
||||
|
||||
workflow test_multiqc {
|
||||
input = [ [ id: 'test', single_end: false ],
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
||||
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
|
||||
]
|
||||
input = [
|
||||
[ id: 'test', single_end: false ],
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
|
||||
]
|
||||
|
||||
FASTQC ( input )
|
||||
MULTIQC ( FASTQC.out.zip.collect { it[1] } )
|
||||
MULTIQC ( FASTQC.out.zip.collect { it[1] }, [[],[]] )
|
||||
}
|
||||
|
||||
workflow test_multiqc_fn_collision {
|
||||
fqc_input = [
|
||||
[ id: 'test', single_end: false ],
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
|
||||
]
|
||||
mqc_input = Channel.empty()
|
||||
|
||||
FASTQC ( fqc_input )
|
||||
mqc_input = mqc_input.mix(FASTQC.out.zip.collect { it[1] })
|
||||
|
||||
FASTQC2 ( fqc_input )
|
||||
mqc_input = mqc_input.mix(FASTQC2.out.zip.collect { it[1] })
|
||||
|
||||
MULTIQC ( mqc_input, [[],[]] )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,5 +1,7 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
withName: "FASTQC*" {
|
||||
publishDir = [ enabled: false ]
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,5 +1,12 @@
|
|||
- name: multiqc
|
||||
command: nextflow run ./tests/modules/multiqc -entry test_multiqc -c ./tests/config/nextflow.config -c ./tests/modules/multiqc/nextflow.config
|
||||
- name: multiqc test_multiqc
|
||||
command: nextflow run ./tests/modules/multiqc -entry test_multiqc -c ./tests/config/nextflow.config -c ./tests/modules/multiqc/nextflow.config
|
||||
tags:
|
||||
- multiqc
|
||||
files:
|
||||
- path: output/multiqc/multiqc_report.html
|
||||
|
||||
- name: multiqc test_multiqc_fn_collision
|
||||
command: nextflow run ./tests/modules/multiqc -entry test_multiqc_fn_collision -c ./tests/config/nextflow.config -c ./tests/modules/multiqc/nextflow.config
|
||||
tags:
|
||||
- multiqc
|
||||
files:
|
||||
|
|
|
|||
40
tests/modules/rhocall/annotate/main.nf
Normal file
40
tests/modules/rhocall/annotate/main.nf
Normal file
|
|
@ -0,0 +1,40 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { RHOCALL_ANNOTATE } from '../../../../modules/rhocall/annotate/main.nf'
|
||||
include { BCFTOOLS_ROH } from '../../../../modules/bcftools/roh/main.nf'
|
||||
|
||||
workflow test_rhocall_annotate {
|
||||
|
||||
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 )
|
||||
RHOCALL_ANNOTATE ( input, BCFTOOLS_ROH.out.roh, [])
|
||||
|
||||
}
|
||||
|
||||
workflow test_rhocall_annotate_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 )
|
||||
RHOCALL_ANNOTATE ( input, BCFTOOLS_ROH.out.roh, [])
|
||||
|
||||
}
|
||||
5
tests/modules/rhocall/annotate/nextflow.config
Normal file
5
tests/modules/rhocall/annotate/nextflow.config
Normal file
|
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
17
tests/modules/rhocall/annotate/test.yml
Normal file
17
tests/modules/rhocall/annotate/test.yml
Normal file
|
|
@ -0,0 +1,17 @@
|
|||
- name: "rhocall annotate"
|
||||
command: nextflow run ./tests/modules/rhocall/annotate -entry test_rhocall_annotate -c ./tests/config/nextflow.config -c ./tests/modules/rhocall/annotate/nextflow.config
|
||||
tags:
|
||||
- "rhocall"
|
||||
- "rhocall/annotate"
|
||||
files:
|
||||
- path: "output/rhocall/test_rhocall.vcf"
|
||||
- path: "output/rhocall/versions.yml"
|
||||
|
||||
- name: "rhocall annotate stub"
|
||||
command: nextflow run ./tests/modules/rhocall/annotate -entry test_rhocall_annotate_stub -c ./tests/config/nextflow.config -c ./tests/modules/rhocall/annotate/nextflow.config -stub-run
|
||||
tags:
|
||||
- "rhocall"
|
||||
- "rhocall/annotate"
|
||||
files:
|
||||
- path: "output/rhocall/test_rhocall.vcf"
|
||||
- path: "output/rhocall/versions.yml"
|
||||
16
tests/modules/snippy/run/main.nf
Normal file
16
tests/modules/snippy/run/main.nf
Normal file
|
|
@ -0,0 +1,16 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { SNIPPY_RUN } from '../../../../modules/snippy/run/main.nf'
|
||||
|
||||
workflow test_snippy_run {
|
||||
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
||||
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
|
||||
]
|
||||
reference = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
||||
SNIPPY_RUN ( input, reference )
|
||||
}
|
||||
5
tests/modules/snippy/run/nextflow.config
Normal file
5
tests/modules/snippy/run/nextflow.config
Normal file
|
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
39
tests/modules/snippy/run/test.yml
Normal file
39
tests/modules/snippy/run/test.yml
Normal file
|
|
@ -0,0 +1,39 @@
|
|||
- name: snippy run test_snippy_run
|
||||
command: |
|
||||
nextflow run tests/modules/snippy/run -entry test_snippy_run -c tests/config/nextflow.config -c tests/modules/snippy/run/nextflow.config
|
||||
tags:
|
||||
- snippy/run
|
||||
- snippy
|
||||
files:
|
||||
- path: output/snippy/test/test.aligned.fa
|
||||
md5sum: 47e3390d4167edf1955d162d37aca5e3
|
||||
- path: output/snippy/test/test.bam
|
||||
- path: output/snippy/test/test.bam.bai
|
||||
- path: output/snippy/test/test.bed
|
||||
- path: output/snippy/test/test.consensus.fa
|
||||
md5sum: 483f4a5dfe60171c86ee9b7e6dff908b
|
||||
- path: output/snippy/test/test.consensus.subs.fa
|
||||
md5sum: 483f4a5dfe60171c86ee9b7e6dff908b
|
||||
- path: output/snippy/test/test.csv
|
||||
md5sum: 322f942115e5945c2041a88246166703
|
||||
- path: output/snippy/test/test.filt.vcf
|
||||
contains: ["fileformat", "freebayes", "CHROM"]
|
||||
- path: output/snippy/test/test.gff
|
||||
md5sum: df19e1b84ba6f691d20c72b397c88abf
|
||||
- path: output/snippy/test/test.html
|
||||
md5sum: 1ccbf0ffcadae1a6b2e11681d24c9938
|
||||
- path: output/snippy/test/test.log
|
||||
contains: ["snippy", "consensus", "subs"]
|
||||
- path: output/snippy/test/test.raw.vcf
|
||||
contains: ["fileformat", "freebayes", "CHROM"]
|
||||
- path: output/snippy/test/test.tab
|
||||
md5sum: beb9bde3bce985e53e8feba9ec5b136e
|
||||
- path: output/snippy/test/test.txt
|
||||
contains: ["DateTime", "ReadFiles", "VariantTotal"]
|
||||
- path: output/snippy/test/test.vcf
|
||||
contains: ["fileformat", "freebayes", "CHROM"]
|
||||
- path: output/snippy/test/test.vcf.gz
|
||||
- path: output/snippy/test/test.vcf.gz.csi
|
||||
md5sum: bed9fa291c220a1ba04eb2d448932ffc
|
||||
- path: output/snippy/versions.yml
|
||||
md5sum: 518aad56c4dbefb6cbcde5ab38cf7b5d
|
||||
|
|
@ -2,22 +2,41 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { TIDDIT_COV } from '../../../../modules/tiddit/cov/main.nf'
|
||||
include { TIDDIT_COV as TIDDIT_COV_BED } from '../../../../modules/tiddit/cov/main.nf'
|
||||
include { TIDDIT_COV as TIDDIT_COV_WIG } from '../../../../modules/tiddit/cov/main.nf'
|
||||
|
||||
workflow test_tiddit_cov {
|
||||
workflow test_tiddit_cov_cram_bed {
|
||||
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ]
|
||||
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
||||
TIDDIT_COV ( input, fasta )
|
||||
TIDDIT_COV_BED ( input, fasta )
|
||||
}
|
||||
|
||||
workflow test_tiddit_cov_no_ref {
|
||||
workflow test_tiddit_cov_bam_bed {
|
||||
|
||||
input = [ [ id:'test', single_end:false ], // 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'], checkIfExists: true) ]
|
||||
|
||||
TIDDIT_COV ( input, [] )
|
||||
TIDDIT_COV_BED ( input, [] )
|
||||
}
|
||||
|
||||
workflow test_tiddit_cov_cram_wig {
|
||||
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
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)
|
||||
|
||||
TIDDIT_COV_WIG ( input, fasta )
|
||||
}
|
||||
|
||||
workflow test_tiddit_cov_bam_wig {
|
||||
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
|
||||
|
||||
TIDDIT_COV_WIG ( input, [] )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,4 +2,8 @@ process {
|
|||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
withName: TIDDIT_COV_WIG {
|
||||
ext.args = '-w'
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,17 +1,35 @@
|
|||
- name: tiddit cov test_tiddit_cov
|
||||
command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
|
||||
- name: tiddit cov test_tiddit_cov_cram_bed
|
||||
command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_cram_bed -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
|
||||
tags:
|
||||
- tiddit
|
||||
- tiddit/cov
|
||||
files:
|
||||
- path: output/tiddit/test.tab
|
||||
md5sum: f7974948f809f94879d8a60b726194f5
|
||||
- path: output/tiddit/test.bed
|
||||
md5sum: 3b1a28c62a5f25bbba77c1042e9abdf7
|
||||
|
||||
- name: tiddit cov test_tiddit_cov_no_ref
|
||||
command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_no_ref -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
|
||||
- name: tiddit cov test_tiddit_cov_bam_bed
|
||||
command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_bam_bed -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
|
||||
tags:
|
||||
- tiddit
|
||||
- tiddit/cov
|
||||
files:
|
||||
- path: output/tiddit/test.tab
|
||||
md5sum: f7974948f809f94879d8a60b726194f5
|
||||
- path: output/tiddit/test.bed
|
||||
md5sum: 9d1474f1c7c6516205254077087bb026
|
||||
|
||||
- name: tiddit cov test_tiddit_cov_cram_wig
|
||||
command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_cram_wig -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
|
||||
tags:
|
||||
- tiddit
|
||||
- tiddit/cov
|
||||
files:
|
||||
- path: output/tiddit/test.wig
|
||||
md5sum: ca3645fd0c3491c86c075c91d16d57c4
|
||||
|
||||
- name: tiddit cov test_tiddit_cov_bam_wig
|
||||
command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_bam_wig -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
|
||||
tags:
|
||||
- tiddit
|
||||
- tiddit/cov
|
||||
files:
|
||||
- path: output/tiddit/test.wig
|
||||
md5sum: 44bea2ac6a56774738e65773065da670
|
||||
|
|
|
|||
|
|
@ -2,25 +2,33 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
|
||||
include { TIDDIT_SV } from '../../../../modules/tiddit/sv/main.nf'
|
||||
|
||||
workflow test_tiddit_sv {
|
||||
input = [
|
||||
workflow test_tiddit_sv_bam {
|
||||
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'], 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)
|
||||
|
||||
TIDDIT_SV ( input, fasta, fai )
|
||||
BWA_INDEX( fasta )
|
||||
|
||||
TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
|
||||
}
|
||||
|
||||
workflow test_tiddit_sv_no_ref {
|
||||
input = [
|
||||
workflow test_tiddit_sv_cram {
|
||||
input = [
|
||||
[ id:'test' ], // meta map
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
|
||||
[ 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) ]
|
||||
]
|
||||
|
||||
TIDDIT_SV ( input, [], [] )
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
||||
BWA_INDEX( fasta )
|
||||
|
||||
TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
|
||||
}
|
||||
|
|
|
|||
Some files were not shown because too many files have changed in this diff Show more
Loading…
Reference in a new issue