mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
Merge branch 'master' into rp3-add-snippy
This commit is contained in:
commit
24ca2ed464
63 changed files with 1136 additions and 185 deletions
|
@ -42,7 +42,6 @@ output:
|
|||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
## TODO nf-core: Delete / customise this example output
|
||||
- out:
|
||||
type: file
|
||||
description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml)
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||||
|
|
|
@ -8,7 +8,7 @@ process BCFTOOLS_CONCAT {
|
|||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
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||||
|
||||
input:
|
||||
tuple val(meta), path(vcfs)
|
||||
tuple val(meta), path(vcfs), path(tbi)
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||||
|
||||
output:
|
||||
tuple val(meta), path("*.gz"), emit: vcf
|
||||
|
|
|
@ -25,6 +25,11 @@ input:
|
|||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- tbi:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more index files (optional)
|
||||
e.g. [ 'file1.tbi', 'file2.tbi' ]
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
|
@ -10,6 +10,7 @@ process CNVKIT_BATCH {
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|||
input:
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tuple val(meta), path(tumor), path(normal)
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path fasta
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path fasta_fai
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path targets
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path reference
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||||
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||||
|
@ -28,48 +29,167 @@ process CNVKIT_BATCH {
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script:
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def args = task.ext.args ?: ''
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||||
|
||||
// execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
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||||
// input pair is assumed to have same extension if both exist
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def is_cram = tumor.Extension == "cram" ? true : false
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def tumor_out = is_cram ? tumor.BaseName + ".bam" : "${tumor}"
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||||
def tumor_exists = tumor ? true : false
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||||
def normal_exists = normal ? true : false
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||||
|
||||
// execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
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def tumor_cram = tumor_exists && tumor.Extension == "cram" ? true : false
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def normal_cram = normal_exists && normal.Extension == "cram" ? true : false
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def tumor_bam = tumor_exists && tumor.Extension == "bam" ? true : false
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def normal_bam = normal_exists && normal.Extension == "bam" ? true : false
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|
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def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}"
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|
||||
// do not run samtools on normal samples in tumor_only mode
|
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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) = ["", "", ""]
|
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def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : ""
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|
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if (normal_exists){
|
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def normal_prefix = normal.BaseName
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normal_out = is_cram ? "${normal_prefix}" + ".bam" : "${normal}"
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normal_args = normal_prefix ? "--normal $normal_out" : ""
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normal_out = normal_cram ? "${normal_prefix}" + ".bam" : "${normal}"
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||||
fasta_args = fasta ? "--fasta $fasta" : ""
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||||
|
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// germline mode
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// normal samples must be input without a flag
|
||||
// requires flag --normal to be empty []
|
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if(!tumor_exists){
|
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tumor_out = "${normal_prefix}" + ".bam"
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normal_args = "--normal "
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}
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// somatic mode
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else {
|
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normal_args = normal_prefix ? "--normal $normal_out" : ""
|
||||
}
|
||||
}
|
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|
||||
def target_args = targets ? "--targets $targets" : ""
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||||
def reference_args = reference ? "--reference $reference" : ""
|
||||
|
||||
"""
|
||||
if $is_cram; then
|
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samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out
|
||||
if $normal_exists; then
|
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samtools view -T $fasta $normal -@ $task.cpus -o $normal_out
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fi
|
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fi
|
||||
// somatic_mode cram_input
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if (tumor_cram && normal_cram){
|
||||
"""
|
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samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out
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samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $normal_out
|
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|
||||
cnvkit.py \\
|
||||
batch \\
|
||||
$tumor_out \\
|
||||
$normal_args \\
|
||||
$fasta_args \\
|
||||
$reference_args \\
|
||||
$target_args \\
|
||||
--processes $task.cpus \\
|
||||
$args
|
||||
cnvkit.py \\
|
||||
batch \\
|
||||
$tumor_out \\
|
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$normal_args \\
|
||||
$fasta_args \\
|
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$reference_args \\
|
||||
$target_args \\
|
||||
--processes $task.cpus \\
|
||||
$args
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|
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
|
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
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cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
// somatic_mode bam_input
|
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else if (tumor_bam && normal_bam){
|
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"""
|
||||
cnvkit.py \\
|
||||
batch \\
|
||||
$tumor_out \\
|
||||
$normal_args \\
|
||||
$fasta_args \\
|
||||
$reference_args \\
|
||||
$target_args \\
|
||||
--processes $task.cpus \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
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"${task.process}":
|
||||
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
|
||||
END_VERSIONS
|
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"""
|
||||
}
|
||||
// tumor_only_mode cram_input
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else if(tumor_cram && !normal_exists){
|
||||
"""
|
||||
samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out
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|
||||
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")
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||||
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}.${GENOME}
|
||||
}
|
||||
|
||||
build_push "GRCh37" "homo_sapiens" "104" "104.3"
|
||||
build_push "GRCh38" "homo_sapiens" "104" "104.3"
|
||||
build_push "GRCm38" "mus_musculus" "102" "104.3"
|
||||
build_push "GRCm39" "mus_musculus" "104" "104.3"
|
||||
build_push "CanFam3.1" "canis_lupus_familiaris" "104" "104.3"
|
||||
build_push "WBcel235" "caenorhabditis_elegans" "104" "104.3"
|
||||
build_push "GRCh37" "homo_sapiens" "105" "105.0"
|
||||
build_push "GRCh38" "homo_sapiens" "105" "105.0"
|
||||
build_push "GRCm38" "mus_musculus" "102" "105.0"
|
||||
build_push "GRCm39" "mus_musculus" "105" "105.0"
|
||||
build_push "CanFam3.1" "canis_lupus_familiaris" "104" "105.0"
|
||||
build_push "WBcel235" "caenorhabditis_elegans" "105" "105.0"
|
||||
|
|
|
@ -1,10 +1,10 @@
|
|||
# You can use this file to create a conda environment for this module:
|
||||
# conda env create -f environment.yml
|
||||
name: nf-core-vep-104.3
|
||||
name: nf-core-vep-105.0
|
||||
channels:
|
||||
- conda-forge
|
||||
- bioconda
|
||||
- defaults
|
||||
|
||||
dependencies:
|
||||
- bioconda::ensembl-vep=104.3
|
||||
- bioconda::ensembl-vep=105.0
|
||||
|
|
|
@ -11,7 +11,7 @@ process FILTLONG {
|
|||
tuple val(meta), path(shortreads), path(longreads)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("${meta.id}_lr_filtlong.fastq.gz"), emit: reads
|
||||
tuple val(meta), path("*.fastq.gz"), emit: reads
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
|
@ -20,13 +20,14 @@ process FILTLONG {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def short_reads = meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
|
||||
def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
|
||||
if ("$longreads" == "${prefix}.fastq.gz") error "Longread FASTQ input and output names are the same, set prefix in module configuration to disambiguate!"
|
||||
"""
|
||||
filtlong \\
|
||||
$short_reads \\
|
||||
$args \\
|
||||
$longreads \\
|
||||
| gzip -n > ${prefix}_lr_filtlong.fastq.gz
|
||||
| gzip -n > ${prefix}.fastq.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
50
modules/gatk4/calibratedragstrmodel/main.nf
Normal file
50
modules/gatk4/calibratedragstrmodel/main.nf
Normal file
|
@ -0,0 +1,50 @@
|
|||
process GATK4_CALIBRATEDRAGSTRMODEL {
|
||||
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(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 \\
|
||||
$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 . \\
|
||||
$args
|
||||
|
||||
|
|
|
@ -32,6 +32,10 @@ input:
|
|||
- intervals:
|
||||
type: file
|
||||
description: Bed file with the genomic regions included in the library (optional)
|
||||
- dragstr_model:
|
||||
type: file
|
||||
description: Text file containing the DragSTR model of the used BAM/CRAM file (optional)
|
||||
pattern: "*.txt"
|
||||
- fasta:
|
||||
type: file
|
||||
description: The reference fasta file
|
||||
|
|
|
@ -13,6 +13,7 @@ process GATK4_MERGEVCFS {
|
|||
|
||||
output:
|
||||
tuple val(meta), path('*.vcf.gz'), emit: vcf
|
||||
tuple val(meta), path("*.tbi") , emit: tbi
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
|
|
|
@ -35,6 +35,11 @@ output:
|
|||
type: file
|
||||
description: merged vcf file
|
||||
pattern: "*.vcf.gz"
|
||||
- tbi:
|
||||
type: file
|
||||
description: index files for the merged vcf files
|
||||
pattern: "*.tbi"
|
||||
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
|
|
@ -2,16 +2,15 @@ process STAR_ALIGN {
|
|||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
// Note: 2.7X indices incompatible with AWS iGenomes.
|
||||
conda (params.enable_conda ? 'bioconda::star=2.7.9a' : null)
|
||||
conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/star:2.7.9a--h9ee0642_0' :
|
||||
'quay.io/biocontainers/star:2.7.9a--h9ee0642_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' :
|
||||
'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path index
|
||||
path gtf
|
||||
path index
|
||||
path gtf
|
||||
val star_ignore_sjdbgtf
|
||||
val seq_platform
|
||||
val seq_center
|
||||
|
@ -67,6 +66,8 @@ process STAR_ALIGN {
|
|||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
star: \$(STAR --version | sed -e "s/STAR_//g")
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
@ -2,19 +2,18 @@ process STAR_GENOMEGENERATE {
|
|||
tag "$fasta"
|
||||
label 'process_high'
|
||||
|
||||
// Note: 2.7X indices incompatible with AWS iGenomes.
|
||||
conda (params.enable_conda ? "bioconda::star=2.7.9a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1c4c32d87798d425c970ececfbadd155e7560277-0' :
|
||||
'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1c4c32d87798d425c970ececfbadd155e7560277-0' }"
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' :
|
||||
'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' }"
|
||||
|
||||
input:
|
||||
path fasta
|
||||
path gtf
|
||||
|
||||
output:
|
||||
path "star" , emit: index
|
||||
path "versions.yml" , emit: versions
|
||||
path "star" , emit: index
|
||||
path "versions.yml", emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
@ -22,7 +21,7 @@ process STAR_GENOMEGENERATE {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def args_list = args.tokenize()
|
||||
def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
|
||||
def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
|
||||
if (args_list.contains('--genomeSAindexNbases')) {
|
||||
"""
|
||||
mkdir star
|
||||
|
|
|
@ -21,12 +21,18 @@ process UNTAR {
|
|||
def args = task.ext.args ?: ''
|
||||
def args2 = task.ext.args2 ?: ''
|
||||
untar = archive.toString() - '.tar.gz'
|
||||
|
||||
"""
|
||||
mkdir output
|
||||
|
||||
tar \\
|
||||
-C output --strip-components 1 \\
|
||||
-xzvf \\
|
||||
$args \\
|
||||
$archive \\
|
||||
$args2 \\
|
||||
$args2
|
||||
|
||||
mv output ${untar}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
67
modules/vsearch/usearchglobal/main.nf
Normal file
67
modules/vsearch/usearchglobal/main.nf
Normal file
|
@ -0,0 +1,67 @@
|
|||
process VSEARCH_USEARCHGLOBAL {
|
||||
tag "${meta.id}"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--h95f258a_0':
|
||||
'quay.io/biocontainers/vsearch:2.21.1--h95f258a_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(queryfasta)
|
||||
path db
|
||||
val idcutoff
|
||||
val outoption
|
||||
val user_columns
|
||||
|
||||
output:
|
||||
tuple val(meta), path('*.aln') , optional: true, emit: aln
|
||||
tuple val(meta), path('*.biom') , optional: true, emit: biom
|
||||
tuple val(meta), path('*.lca') , optional: true, emit: lca
|
||||
tuple val(meta), path('*.mothur') , optional: true, emit: mothur
|
||||
tuple val(meta), path('*.otu') , optional: true, emit: otu
|
||||
tuple val(meta), path('*.sam') , optional: true, emit: sam
|
||||
tuple val(meta), path('*.tsv') , optional: true, emit: tsv
|
||||
tuple val(meta), path('*.txt') , optional: true, emit: txt
|
||||
tuple val(meta), path('*.uc') , optional: true, emit: uc
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def columns = user_columns ? "--userfields ${user_columns}" : ''
|
||||
switch ( outoption ) {
|
||||
case "alnout": outfmt = "--alnout"; out_ext = 'aln'; break
|
||||
case "biomout": outfmt = "--biomout"; out_ext = 'biom'; break
|
||||
case "blast6out": outfmt = "--blast6out"; out_ext = 'txt'; break
|
||||
case "mothur_shared_out": outfmt = "--mothur_shared_out"; out_ext = 'mothur'; break
|
||||
case "otutabout": outfmt = "--otutabout"; out_ext = 'otu'; break
|
||||
case "samout": outfmt = "--samout"; out_ext = 'sam'; break
|
||||
case "uc": outfmt = "--uc"; out_ext = 'uc'; break
|
||||
case "userout": outfmt = "--userout"; out_ext = 'tsv'; break
|
||||
case "lcaout": outfmt = "--lcaout"; out_ext = 'lca'; break
|
||||
default:
|
||||
outfmt = "--alnout";
|
||||
out_ext = 'aln';
|
||||
log.warn("Unknown output file format provided (${outoption}): selecting pairwise alignments (alnout)");
|
||||
break
|
||||
}
|
||||
"""
|
||||
vsearch \\
|
||||
--usearch_global $queryfasta \\
|
||||
--db $db \\
|
||||
--id $idcutoff \\
|
||||
--threads $task.cpus \\
|
||||
$args \\
|
||||
${columns} \\
|
||||
${outfmt} ${prefix}.${out_ext}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
vsearch: \$(vsearch --version 2>&1 | head -n 1 | sed 's/vsearch //g' | sed 's/,.*//g' | sed 's/^v//' | sed 's/_.*//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
83
modules/vsearch/usearchglobal/meta.yml
Normal file
83
modules/vsearch/usearchglobal/meta.yml
Normal file
|
@ -0,0 +1,83 @@
|
|||
name: "vsearch_usearchglobal"
|
||||
description: Compare target sequences to fasta-formatted query sequences using global pairwise alignment.
|
||||
keywords:
|
||||
- vsearch
|
||||
- usearch
|
||||
- alignment
|
||||
- fasta
|
||||
tools:
|
||||
- "vsearch":
|
||||
description: "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)"
|
||||
homepage: "https://github.com/torognes/vsearch"
|
||||
documentation: "None"
|
||||
tool_dev_url: "https://github.com/torognes/vsearch"
|
||||
doi: "doi: 10.7717/peerj.2584"
|
||||
licence: "['GPL v3-or-later OR BSD-2-clause']"
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: Groovy Map containing sample information e.g. [ id:'test' ]
|
||||
- queryfasta:
|
||||
type: file
|
||||
description: Query sequences in FASTA format
|
||||
pattern: "*.{fasta,fa,fna,faa}"
|
||||
- db:
|
||||
type: file
|
||||
description: Reference database file in FASTA or UDB format
|
||||
pattern: "*"
|
||||
- idcutoff:
|
||||
type: real
|
||||
description: Reject the sequence match if the pairwise identity is lower than the given id cutoff value (value ranging from 0.0 to 1.0 included)
|
||||
- outoption:
|
||||
type: string
|
||||
description: Specify the type of output file to be generated by selecting one of the vsearch output file options
|
||||
pattern: "alnout|biomout|blast6out|mothur_shared_out|otutabout|samout|uc|userout|lcaout"
|
||||
- user_columns:
|
||||
type: string
|
||||
description: If using the `userout` option, specify which columns to include in output, with fields separated with `+` (e.g. query+target+id). See USEARCH manual for valid options. For other output options, use an empty string.
|
||||
|
||||
output:
|
||||
- aln:
|
||||
type: file
|
||||
description: Results in pairwise alignment format
|
||||
pattern: "*.{aln}"
|
||||
- biom:
|
||||
type: file
|
||||
description: Results in an OTU table in the biom version 1.0 file format
|
||||
pattern: "*.{biom}"
|
||||
- lca:
|
||||
type: file
|
||||
description: Last common ancestor (LCA) information about the hits of each query in tab-separated format
|
||||
pattern: "*.{lca}"
|
||||
- mothur:
|
||||
type: file
|
||||
description: Results in an OTU table in the mothur ’shared’ tab-separated plain text file format
|
||||
pattern: "*.{mothur}"
|
||||
- otu:
|
||||
type: file
|
||||
description: Results in an OTU table in the classic tab-separated plain text format
|
||||
pattern: "*.{otu}"
|
||||
- sam:
|
||||
type: file
|
||||
description: Results written in sam format
|
||||
pattern: "*.{sam}"
|
||||
- tsv:
|
||||
type: file
|
||||
description: Results in tab-separated output, columns defined by user
|
||||
pattern: "*.{tsv}"
|
||||
- txt:
|
||||
type: file
|
||||
description: Tab delimited results in blast-like tabular format
|
||||
pattern: "*.{txt}"
|
||||
- uc:
|
||||
type: file
|
||||
description: Tab delimited results in a uclust-like format with 10 columns
|
||||
pattern: "*.{uc}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
|
||||
authors:
|
||||
- "@jtangrot"
|
|
@ -743,6 +743,10 @@ 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/**
|
||||
|
@ -751,6 +755,10 @@ 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/**
|
||||
|
@ -2056,6 +2064,10 @@ vcftools:
|
|||
- modules/vcftools/**
|
||||
- tests/modules/vcftools/**
|
||||
|
||||
vsearch/usearchglobal:
|
||||
- modules/vsearch/usearchglobal/**
|
||||
- tests/modules/vsearch/usearchglobal/**
|
||||
|
||||
yara/index:
|
||||
- modules/yara/index/**
|
||||
- tests/modules/yara/index/**
|
||||
|
|
|
@ -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"
|
||||
|
|
|
@ -4,13 +4,25 @@ nextflow.enable.dsl = 2
|
|||
|
||||
include { BCFTOOLS_CONCAT } from '../../../../modules/bcftools/concat/main.nf'
|
||||
|
||||
workflow test_bcftools_concat {
|
||||
workflow test_bcftools_concat_tbi {
|
||||
|
||||
input = [ [ id:'test3' ], // meta map
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
|
||||
file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ]
|
||||
file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
|
||||
file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) ]
|
||||
]
|
||||
|
||||
BCFTOOLS_CONCAT ( input )
|
||||
}
|
||||
|
||||
workflow test_bcftools_concat_no_tbi {
|
||||
|
||||
input = [ [ id:'test3' ], // meta map
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
|
||||
file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
|
||||
[]
|
||||
]
|
||||
|
||||
|
||||
BCFTOOLS_CONCAT ( input )
|
||||
}
|
||||
|
|
|
@ -1,8 +1,17 @@
|
|||
- name: bcftools concat test_bcftools_concat
|
||||
command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config
|
||||
- name: bcftools concat test_bcftools_concat_tbi
|
||||
command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config
|
||||
tags:
|
||||
- bcftools/concat
|
||||
- bcftools
|
||||
- bcftools/concat
|
||||
files:
|
||||
- path: output/bcftools/test3.vcf.gz
|
||||
md5sum: 35c88bfaad20101062e98beb217d7137
|
||||
|
||||
- name: bcftools concat test_bcftools_concat_no_tbi
|
||||
command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_no_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config
|
||||
tags:
|
||||
- bcftools
|
||||
- bcftools/concat
|
||||
files:
|
||||
- path: output/bcftools/test3.vcf.gz
|
||||
md5sum: 35c88bfaad20101062e98beb217d7137
|
||||
|
|
|
@ -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
|
||||
|
|
|
@ -2,4 +2,7 @@ process {
|
|||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
ext.args = "--min_length 10"
|
||||
ext.prefix = "test_lr"
|
||||
|
||||
}
|
||||
|
|
|
@ -1,23 +1,26 @@
|
|||
- name: filtlong test_filtlong
|
||||
command: nextflow run ./tests/modules/filtlong -entry test_filtlong -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
|
||||
command: nextflow run ./tests/modules/filtlong -entry test_filtlong -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
|
||||
tags:
|
||||
- filtlong
|
||||
files:
|
||||
- path: output/filtlong/test_lr_filtlong.fastq.gz
|
||||
md5sum: 7029066c27ac6f5ef18d660d5741979a
|
||||
- path: output/filtlong/test_lr.fastq.gz
|
||||
contains:
|
||||
- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
|
||||
|
||||
- name: filtlong test_filtlong_illumina_se
|
||||
command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
|
||||
command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
|
||||
tags:
|
||||
- filtlong
|
||||
files:
|
||||
- path: output/filtlong/test_lr_filtlong.fastq.gz
|
||||
md5sum: 7029066c27ac6f5ef18d660d5741979a
|
||||
- path: output/filtlong/test_lr.fastq.gz
|
||||
contains:
|
||||
- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
|
||||
|
||||
- name: filtlong test_filtlong_illumina_pe
|
||||
command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
|
||||
command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
|
||||
tags:
|
||||
- filtlong
|
||||
files:
|
||||
- path: output/filtlong/test_lr_filtlong.fastq.gz
|
||||
md5sum: 7029066c27ac6f5ef18d660d5741979a
|
||||
- path: output/filtlong/test_lr.fastq.gz
|
||||
contains:
|
||||
- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
|
||||
|
|
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/calibratedragstrmodel
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.txt
|
||||
md5sum: 0a1a1583b157fa2251dd931ed165da4f
|
||||
|
||||
- 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/calibratedragstrmodel
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.txt
|
||||
md5sum: 1aa7ab38023f724877b3323c5e6b9a4e
|
||||
|
||||
- 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/calibratedragstrmodel
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.txt
|
||||
md5sum: def8baccad7bd59006f08fcb0a6721bf
|
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
|
||||
|
|
|
@ -6,6 +6,8 @@
|
|||
files:
|
||||
- path: output/gatk4/test.vcf.gz
|
||||
md5sum: 5b289bda88d3a3504f2e19ee8cff177c
|
||||
- path: output/gatk4/test.vcf.gz.tbi
|
||||
md5sum: a81673763b13086cfce9a23e72a35a16
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 mergevcfs test_gatk4_mergevcfs_no_dict
|
||||
|
|
|
@ -36,7 +36,7 @@
|
|||
- path: output/star/star/transcriptInfo.tab
|
||||
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
|
||||
- path: output/star/test.Aligned.out.bam
|
||||
md5sum: b9f5e2f6a624b64c300fe25dc3ac801f
|
||||
md5sum: 63de6af2210e138b49d7b4d570c6e67f
|
||||
- path: output/star/test.Log.final.out
|
||||
- path: output/star/test.Log.out
|
||||
- path: output/star/test.Log.progress.out
|
||||
|
@ -80,7 +80,7 @@
|
|||
- path: output/star/star/transcriptInfo.tab
|
||||
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
|
||||
- path: output/star/test.Aligned.out.bam
|
||||
md5sum: 38d08f0b944a2a1b981a250d675aa0d9
|
||||
md5sum: 7cdef439bc8092bfefb4d091bf8ee6ab
|
||||
- path: output/star/test.Log.final.out
|
||||
- path: output/star/test.Log.out
|
||||
- path: output/star/test.Log.progress.out
|
||||
|
@ -124,7 +124,7 @@
|
|||
- path: output/star/star/transcriptInfo.tab
|
||||
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
|
||||
- path: output/star/test.Aligned.out.bam
|
||||
md5sum: c740d5177067c1fcc48ab7a16cd639d7
|
||||
md5sum: 5dbc36fce7b72628c809bbc7d3d67973
|
||||
- path: output/star/test.Log.final.out
|
||||
- path: output/star/test.Log.out
|
||||
- path: output/star/test.Log.progress.out
|
||||
|
@ -168,9 +168,9 @@
|
|||
- path: output/star/star/transcriptInfo.tab
|
||||
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
|
||||
- path: output/star/test.Aligned.out.bam
|
||||
md5sum: a1bd1b40950a58ea2776908076160052
|
||||
md5sum: d85858bf55a523121dde762046a34c5c
|
||||
- path: output/star/test.Chimeric.out.junction
|
||||
md5sum: 327629eb54032212f29e1c32cbac6975
|
||||
md5sum: ae87d1a24180f5a35cf6b47fdfdd0539
|
||||
- path: output/star/test.Log.final.out
|
||||
- path: output/star/test.Log.out
|
||||
- path: output/star/test.Log.progress.out
|
||||
|
|
|
@ -12,3 +12,13 @@ workflow test_untar {
|
|||
|
||||
UNTAR ( input )
|
||||
}
|
||||
|
||||
|
||||
workflow test_untar_different_output_path {
|
||||
input = [
|
||||
[],
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)
|
||||
]
|
||||
|
||||
UNTAR ( input )
|
||||
}
|
||||
|
|
|
@ -1,5 +1,5 @@
|
|||
- name: untar
|
||||
command: nextflow run ./tests/modules/untar -entry test_untar -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config
|
||||
- name: untar test_untar
|
||||
command: nextflow run ./tests/modules/untar -entry test_untar -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config
|
||||
tags:
|
||||
- untar
|
||||
files:
|
||||
|
@ -9,3 +9,11 @@
|
|||
md5sum: a033d00cf6759407010b21700938f543
|
||||
- path: output/untar/kraken2/taxo.k2d
|
||||
md5sum: 094d5891cdccf2f1468088855c214b2c
|
||||
|
||||
- name: untar test_untar_different_output_path
|
||||
command: nextflow run ./tests/modules/untar -entry test_untar_different_output_path -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config
|
||||
tags:
|
||||
- untar
|
||||
files:
|
||||
- path: output/untar/flowcell/RunInfo.xml
|
||||
md5sum: 03038959f4dd181c86bc97ae71fe270a
|
||||
|
|
25
tests/modules/vsearch/usearchglobal/main.nf
Normal file
25
tests/modules/vsearch/usearchglobal/main.nf
Normal file
|
@ -0,0 +1,25 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { VSEARCH_USEARCHGLOBAL } from '../../../../modules/vsearch/usearchglobal/main.nf'
|
||||
|
||||
workflow test_vsearch_usearchglobal {
|
||||
|
||||
query = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
|
||||
db = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
idcutoff = 0.985
|
||||
outoption = "xcfert" // Nonsense text to check default case.
|
||||
columns = ""
|
||||
VSEARCH_USEARCHGLOBAL ( [[id:'test'], query], db, idcutoff, outoption, columns )
|
||||
}
|
||||
|
||||
workflow test_vsearch_usearchglobal_userout {
|
||||
|
||||
query = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
|
||||
db = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
idcutoff = 0.985
|
||||
outoption = "userout"
|
||||
columns = "query+target+id"
|
||||
VSEARCH_USEARCHGLOBAL ( [[id:'test'], query], db, idcutoff, outoption, columns )
|
||||
}
|
4
tests/modules/vsearch/usearchglobal/nextflow.config
Normal file
4
tests/modules/vsearch/usearchglobal/nextflow.config
Normal file
|
@ -0,0 +1,4 @@
|
|||
process {
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
}
|
||||
|
26
tests/modules/vsearch/usearchglobal/test.yml
Normal file
26
tests/modules/vsearch/usearchglobal/test.yml
Normal file
|
@ -0,0 +1,26 @@
|
|||
- name: vsearch usearchglobal test_vsearch_usearchglobal
|
||||
command: nextflow run ./tests/modules/vsearch/usearchglobal -entry test_vsearch_usearchglobal -c ./tests/config/nextflow.config -c ./tests/modules/vsearch/usearchglobal/nextflow.config
|
||||
tags:
|
||||
- vsearch/usearchglobal
|
||||
- vsearch
|
||||
files:
|
||||
- path: output/vsearch/test.aln
|
||||
contains:
|
||||
- "vsearch --usearch_global transcriptome.fasta --db genome.fasta --id 0.985 --threads 2 --alnout test.aln"
|
||||
- "Query >lcl|MT192765.1_cds_QIK50427.1_2"
|
||||
- "%Id TLen Target"
|
||||
- "100% 29829 MT192765.1"
|
||||
- "Query 3822nt >lcl|MT192765.1_cds_QIK50427.1_2"
|
||||
- "Target 29829nt >MT192765.1"
|
||||
- "Qry 21249 + CAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAA 21291"
|
||||
- "Tgt 21506 + CAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAA 21548"
|
||||
- "21291 cols, 21290 ids (100.0%), 1 gaps (0.0%)"
|
||||
|
||||
- name: vsearch usearchglobal test_vsearch_usearchglobal_userout
|
||||
command: nextflow run ./tests/modules/vsearch/usearchglobal -entry test_vsearch_usearchglobal_userout -c ./tests/config/nextflow.config -c ./tests/modules/vsearch/usearchglobal/nextflow.config
|
||||
tags:
|
||||
- vsearch/usearchglobal
|
||||
- vsearch
|
||||
files:
|
||||
- path: output/vsearch/test.tsv
|
||||
md5sum: b6cc50f7c8d18cb82e74dab70ed4baab
|
Loading…
Reference in a new issue