Merge branch 'master' into haplocheck

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Taniguti 2022-06-10 20:39:33 -03:00 committed by GitHub
commit 547f483b74
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50 changed files with 1023 additions and 66 deletions

48
modules/ampir/main.nf Normal file
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@ -0,0 +1,48 @@
process AMPIR {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/r-ampir:1.1.0':
'quay.io/biocontainers/r-ampir:1.1.0' }"
input:
tuple val(meta), path(faa)
val model
val min_length
val min_probability
output:
tuple val(meta), path("*.faa"), emit: amps_faa
tuple val(meta), path("*.tsv"), emit: amps_tsv
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
min_length = ("${min_length}" == "[]") ? "": " min_len = as.integer(${min_length})," // Fall back to AMPir default value if none specified
if ("$faa" == "${prefix}.faa") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
"""
#!/usr/bin/env Rscript
library(ampir)
input_seqs <- read_faa('${faa}')
prediction <- predict_amps(input_seqs,${min_length} model = '${model}')
prediction <- prediction[which(prediction\$prob_AMP >= as.numeric(${min_probability})), ]
output_seqs <- input_seqs[row.names(prediction), ]
write.table(prediction, file = "${prefix}.tsv", row.names = FALSE, sep = "\t", quote = FALSE, dec = '.')
df_to_faa(output_seqs, "${prefix}.faa")
version_file_path <- "versions.yml"
version_ampir <- paste(unlist(packageVersion("ampir")), collapse = ".")
f <- file(version_file_path, "w")
writeLines('"${task.process}":', f)
writeLines(" ampir: ", f, sep = "")
writeLines(version_ampir, f)
close(f)
"""
}

59
modules/ampir/meta.yml Normal file
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@ -0,0 +1,59 @@
name: "ampir"
description: A fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs.
keywords:
- ampir
- amp
- antimicrobial peptide prediction
tools:
- "ampir":
description: "A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale."
homepage: "https://github.com/Legana/ampir"
documentation: "https://cran.r-project.org/web/packages/ampir/index.html"
tool_dev_url: "https://github.com/Legana/ampir"
doi: "10.1093/bioinformatics/btaa653"
licence: ["GPL v2"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- faa:
type: file
description: FASTA file containing amino acid sequences
pattern: "*.{faa,fasta}"
- model:
type: value
description: Built-in model for AMP prediction
pattern: "{precursor,mature}"
- min_length:
type: value
description: Minimum protein length for which predictions will be generated
pattern: "[0-9]+"
- min_probability:
type: value
description: Cut-off for AMP prediction
pattern: "[0-9][0-9]"
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"
- amps_faa:
type: file
description: File containing AMP predictions in amino acid FASTA format
pattern: "*.{faa}"
- amps_tsv:
type: file
description: File containing AMP predictions in TSV format
pattern: "*.tsv"
authors:
- "@jasmezz"

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@ -1,4 +1,4 @@
# Dockerfile to create container with Cell Ranger v6.1.2
# Dockerfile to create container with Cell Ranger v7.0.0
# Push to nfcore/cellranger:<VER>
FROM continuumio/miniconda3:4.8.2

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@ -5,7 +5,7 @@ process CELLRANGER_COUNT {
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
container "nfcore/cellranger:6.1.2"
container "nfcore/cellranger:7.0.0"
input:
tuple val(meta), path(reads)

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@ -1,4 +1,4 @@
# Dockerfile to create container with Cell Ranger v6.1.2 and bcl2fastq v2.20.0
# Dockerfile to create container with Cell Ranger v7.0.0 and bcl2fastq v2.20.0
# Push to nfcore/cellrangermkfastq:<VER>
FROM continuumio/miniconda3:4.8.2
@ -17,7 +17,7 @@ RUN apt-get update --allow-releaseinfo-change \
# Copy pre-downloaded bcl2fastq2 and cellranger file
ENV BCL2FASTQ2_VER=v2-20-0-linux-x86-64 \
CELLRANGER_VER=6.1.2
CELLRANGER_VER=7.0.0
COPY bcl2fastq2-$BCL2FASTQ2_VER.zip /tmp/bcl2fastq2-$BCL2FASTQ2_VER.zip
COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz

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@ -5,7 +5,7 @@ process CELLRANGER_MKFASTQ {
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
container "nfcore/cellrangermkfastq:6.1.2"
container "nfcore/cellrangermkfastq:7.0.0"
input:
path bcl

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@ -5,7 +5,7 @@ process CELLRANGER_MKGTF {
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
container "nfcore/cellranger:6.1.2"
container "nfcore/cellranger:7.0.0"
input:
path gtf

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@ -5,7 +5,7 @@ process CELLRANGER_MKREF {
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
container "nfcore/cellranger:6.1.2"
container "nfcore/cellranger:7.0.0"
input:
path fasta

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@ -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 \\

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@ -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: |

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@ -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
"""
}

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@ -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"

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

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

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@ -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)

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@ -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)

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

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

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

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

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@ -0,0 +1,40 @@
process SEXDETERRMINE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/sexdeterrmine:1.1.2--hdfd78af_1':
'quay.io/biocontainers/sexdeterrmine:1.1.2--hdfd78af_1' }"
input:
tuple val(meta), path(depth)
path sample_list_file
output:
tuple val(meta), path("*.json"), emit: json
tuple val(meta), path("*.tsv") , emit: tsv
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def sample_list = sample_list_file ? '-f ${sample_list_file}' : ''
if ("$depth" == "${prefix}.tsv") error "Input depth and output TSV names are the same, set prefix in module configuration to disambiguate!"
"""
sexdeterrmine \\
-I $depth \\
$sample_list \\
$args \\
> ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
sexdeterrmine: \$(echo \$(sexdeterrmine --version 2>&1))
END_VERSIONS
"""
}

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@ -0,0 +1,48 @@
name: "sexdeterrmine"
description: Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars.
keywords:
- sex determination
- genetic sex
- relative coverage
- ancient dna
tools:
- "sexdeterrmine":
description: "A python script carry out calculate the relative coverage of X and Y chromosomes, and their associated error bars, out of capture data."
homepage: "https://github.com/TCLamnidis/Sex.DetERRmine"
documentation: "https://github.com/TCLamnidis/Sex.DetERRmine/README.md"
tool_dev_url: "https://github.com/TCLamnidis/Sex.DetERRmine"
doi: "https://doi.org/10.1038/s41467-018-07483-5"
licence: "['GPL v3']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- depth:
type: file
description: Output from samtools depth (with header)
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"
- json:
type: file
description: JSON formatted table of relative coverages on the X and Y, with associated error bars.
pattern: "*.json"
- tsv:
type: file
description: TSV table of relative coverages on the X and Y, with associated error bars.
pattern: "*.tsv"
authors:
- "@TCLamnidis"

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@ -26,6 +26,10 @@ allelecounter:
- modules/allelecounter/**
- tests/modules/allelecounter/**
ampir:
- modules/ampir/**
- tests/modules/ampir/**
amplify/predict:
- modules/amplify/predict/**
- tests/modules/amplify/predict/**
@ -715,6 +719,14 @@ 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/**
@ -851,6 +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/**
@ -1843,6 +1859,10 @@ seqwish/induce:
- modules/seqwish/induce/**
- tests/modules/seqwish/induce/**
sexdeterrmine:
- modules/sexdeterrmine/**
- tests/modules/sexdeterrmine/**
shasum:
- modules/shasum/**
- tests/modules/shasum/**

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@ -232,10 +232,11 @@ params {
test2_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
test2_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
mitochon_standin_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
mitochon_standin_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
test3_single_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam"
test_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
test_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
test_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"

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@ -0,0 +1,20 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { AMPIR } from '../../../modules/ampir/main.nf'
workflow test_ampir {
fasta = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true),
]
model = "precursor"
min_length = []
min_probability = "0.7"
AMPIR ( fasta, model, min_length, min_probability )
}

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

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@ -0,0 +1,11 @@
- name: ampir test_ampir
command: nextflow run ./tests/modules/ampir -entry test_ampir -c ./tests/config/nextflow.config -c ./tests/modules/ampir/nextflow.config
tags:
- ampir
files:
- path: output/ampir/test.tsv
contains: ["seq_name\tseq_aa\tprob_AMP", "WP_014895017.1"]
- path: output/ampir/test.faa
md5sum: 0435609144022c55ac196db053f0df89
- path: output/ampir/versions.yml
md5sum: 4a11d25b8a904a7ffb34ae88f6826888

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@ -1,19 +1,65 @@
- name: cellranger count test_cellranger_count
command: nextflow run tests/modules/cellranger/count -entry test_cellranger_count -c tests/config/nextflow.config -c tests/modules/cellranger/count/nextflow.config
command: nextflow run ./tests/modules/cellranger/count -entry test_cellranger_count -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/count/nextflow.config
tags:
- cellranger
- cellranger/count
- cellranger
files:
- path: output/cellranger/genome.filtered.gtf
md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b
- path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa
md5sum: f315020d899597c1b57e5fe9f60f4c3e
- path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa.fai
md5sum: 3520cd30e1b100e55f578db9c855f685
- path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf.gz
md5sum: d1e05cd46684fa26d852b6bc9f05e31f
- path: output/cellranger/homo_sapiens_chr22_reference/reference.json
md5sum: 8405fd7f527a944eafb9c2909045840b
- path: output/cellranger/homo_sapiens_chr22_reference/star/Genome
md5sum: 897cec2d191945335f8b320438bd9135
- path: output/cellranger/homo_sapiens_chr22_reference/star/SA
md5sum: 7961129ac5d0e1706105be1d31c6b30c
- path: output/cellranger/homo_sapiens_chr22_reference/star/SAindex
md5sum: dcceb480b30cda93fb8c63ddc339093b
- path: output/cellranger/homo_sapiens_chr22_reference/star/chrLength.txt
md5sum: c81f40f27e72606d7d07097c1d56a5b5
- path: output/cellranger/homo_sapiens_chr22_reference/star/chrName.txt
md5sum: 5ae68a67b70976ee95342a7451cb5af1
- path: output/cellranger/homo_sapiens_chr22_reference/star/chrNameLength.txt
md5sum: b190587cae0531f3cf25552d8aa674db
- path: output/cellranger/homo_sapiens_chr22_reference/star/chrStart.txt
md5sum: bc73df776dd3d5bb9cfcbcba60880519
- path: output/cellranger/homo_sapiens_chr22_reference/star/exonGeTrInfo.tab
md5sum: 9129691eeb4ed0d02b17be879fa3edb0
- path: output/cellranger/homo_sapiens_chr22_reference/star/exonInfo.tab
md5sum: 209b82f0683efd03e17d2c729676554f
- path: output/cellranger/homo_sapiens_chr22_reference/star/geneInfo.tab
md5sum: 02a8f4575bdfcd4a42b4d8d07f2e9369
- path: output/cellranger/homo_sapiens_chr22_reference/star/genomeParameters.txt
- path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbInfo.txt
md5sum: 1082ab459363b3f2f7aabcef0979c1ed
- path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.fromGTF.out.tab
- path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.out.tab
- path: output/cellranger/homo_sapiens_chr22_reference/star/transcriptInfo.tab
md5sum: cedcb5f4e7d97bc548cd5daa022e092c
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix.h5
md5sum: f8b6b7cc8248151a98c46d4ebec450c6
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/features.tsv.gz
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/matrix.mtx.gz
- path: output/cellranger/sample-123/outs/metrics_summary.csv
md5sum: 707df0f101d479d93f412ca74f9c4131
- path: output/cellranger/sample-123/outs/molecule_info.h5
md5sum: 0e56836ef0725f2ab05f56ca5a71e55b
md5sum: a13bd7425f441c8d0eac8ffc50082996
- path: output/cellranger/sample-123/outs/possorted_genome_bam.bam
md5sum: 15441da9cfceea0bb48c8b66b1b860df
- path: output/cellranger/sample-123/outs/possorted_genome_bam.bam.bai
md5sum: 7c3d49c77016a09535aff61a027f750c
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix.h5
md5sum: cdad1cd7b215d7137cf92515e81a8525
md5sum: a5290f3e300a4070f3d68a0c2e215f54
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/barcodes.tsv.gz
md5sum: 5cc39ef0c7ac85f2b758b164aabf9157
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/features.tsv.gz
md5sum: 07d497c7ce3e22f374af7b2cf9b97d72
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/matrix.mtx.gz
md5sum: bdce94a51f16e22d40301724080b76ee
- path: output/cellranger/sample-123/outs/web_summary.html

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@ -5,7 +5,6 @@
- cellranger/mkfastq
files:
- path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
md5sum: d41d8cd98f00b204e9800998ecf8427e
- name: cellranger mkfastq test_cellranger_mkfastq_illumina
command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_illumina -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config -stub-run
tags:
@ -13,4 +12,3 @@
- cellranger/mkfastq
files:
- path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
md5sum: d41d8cd98f00b204e9800998ecf8427e

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@ -1,8 +1,8 @@
- name: cellranger mkgtf test_cellranger_mkgtf
command: nextflow run tests/modules/cellranger/mkgtf -entry test_cellranger_mkgtf -c tests/config/nextflow.config -c tests/modules/cellranger/mkgtf/nextflow.config
command: nextflow run ./tests/modules/cellranger/mkgtf -entry test_cellranger_mkgtf -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/mkgtf/nextflow.config
tags:
- cellranger
- cellranger/mkgtf
- cellranger
files:
- path: output/cellranger/genome.filtered.gtf
md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b

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@ -1,8 +1,8 @@
- name: cellranger mkref test_cellranger_mkref
command: nextflow run ./tests/modules/cellranger/mkref -entry test_cellranger_mkref -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/mkref/nextflow.config
tags:
- cellranger
- cellranger/mkref
- cellranger
files:
- path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa
md5sum: f315020d899597c1b57e5fe9f60f4c3e
@ -11,7 +11,7 @@
- path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf.gz
md5sum: 6d9b5f409bfea95022bc25b9590e194e
- path: output/cellranger/homo_sapiens_chr22_reference/reference.json
md5sum: 5d8d1669cd251433505f183e1c9ed6bc
md5sum: 6cc817f0923062e780e6573806840cea
- path: output/cellranger/homo_sapiens_chr22_reference/star/Genome
md5sum: 22102926fadf5890e905ca71b2da3f35
- path: output/cellranger/homo_sapiens_chr22_reference/star/SA

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@ -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", [], [], [] )
}

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@ -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:

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@ -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, [] )
}

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

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@ -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

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@ -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, [] )
}

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

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

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@ -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

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@ -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)
]
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 )
}

View file

@ -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

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@ -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

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@ -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 )
}

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

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@ -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

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@ -0,0 +1,16 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_DEPTH } from '../../../modules/samtools/depth/main.nf'
include { SEXDETERRMINE } from '../../../modules/sexdeterrmine/main.nf'
workflow test_sexdeterrmine {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test3_single_end_markduplicates_sorted_bam'], checkIfExists: true) ]
SAMTOOLS_DEPTH ( input )
SEXDETERRMINE ( SAMTOOLS_DEPTH.out.tsv, [] )
}

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@ -0,0 +1,12 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName:SAMTOOLS_DEPTH {
ext.args = "-H"
}
withName:SEXDETERRMINE {
ext.prefix = { "${meta.id}_sexdet" }
}
}

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@ -0,0 +1,15 @@
- name: sexdeterrmine test_sexdeterrmine
command: nextflow run tests/modules/sexdeterrmine -entry test_sexdeterrmine -c tests/config/nextflow.config
tags:
- sexdeterrmine
files:
- path: output/samtools/test.tsv
md5sum: fa2992ca1ea93a6e1b3e838476191935
- path: output/samtools/versions.yml
md5sum: dbd04b700335c8ad236bd667254c8dd8
- path: output/sexdeterrmine/sexdeterrmine.json
md5sum: bafb2419bb8630eda29a251c20e97166
- path: output/sexdeterrmine/test_sexdet.tsv
md5sum: 1cf8a2b97b38353eb97a96ab872dcca9
- path: output/sexdeterrmine/versions.yml
md5sum: 077361101e8e7997aec3da8a01e59eee

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@ -56,5 +56,5 @@ def test_ensure_valid_version_yml(workflow_dir):
assert len(software_versions), "There must be at least one version emitted."
for tool, version in software_versions.items():
assert re.match(
r"^\d+.*", str(version)
), f"Version number for {tool} must start with a number. "
r"^\d.*|^[a-f0-9]{40}$", str(version)
), f"Version number for {tool} must start with a number, or be a Git SHA commit id. "