Merge branch 'master' into feat/update_cnvpytor

This commit is contained in:
Ramprasad Neethiraj 2022-05-06 00:10:05 +02:00 committed by GitHub
commit 1a3f18d012
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51 changed files with 749 additions and 141 deletions

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@ -8,13 +8,14 @@ LABEL \
COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/nf-core-vep-104.3/bin:$PATH
# Setup default ARG variables
ARG GENOME=GRCh38
ARG SPECIES=homo_sapiens
ARG VEP_VERSION=99
ARG VEP_VERSION=104
ARG VEP_TAG=104.3
# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/nf-core-vep-${VEP_TAG}/bin:$PATH
# Download Genome
RUN vep_install \
@ -27,4 +28,4 @@ RUN vep_install \
--NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE
# Dump the details of the installed packages to a file for posterity
RUN conda env export --name nf-core-vep-104.3 > nf-core-vep-104.3.yml
RUN conda env export --name nf-core-vep-${VEP_TAG} > nf-core-vep-${VEP_TAG}.yml

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@ -10,11 +10,12 @@ build_push() {
VEP_TAG=$4
docker build \
. \
-t nfcore/vep:${VEP_TAG}.${GENOME} \
software/vep/. \
--build-arg GENOME=${GENOME} \
--build-arg SPECIES=${SPECIES} \
--build-arg VEP_VERSION=${VEP_VERSION}
--build-arg VEP_VERSION=${VEP_VERSION} \
--build-arg VEP_TAG=${VEP_TAG}
docker push nfcore/vep:${VEP_TAG}.${GENOME}
}

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@ -13,6 +13,7 @@ process ENSEMBLVEP {
val species
val cache_version
path cache
path extra_files
output:
tuple val(meta), path("*.ann.vcf"), emit: vcf

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@ -10,17 +10,6 @@ tools:
homepage: https://www.ensembl.org/info/docs/tools/vep/index.html
documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html
licence: ["Apache-2.0"]
params:
- use_cache:
type: boolean
description: |
Enable the usage of containers with cache
Does not work with conda
- vep_tag:
type: value
description: |
Specify the tag for the container
https://hub.docker.com/r/nfcore/vep/tags
input:
- meta:
type: map
@ -47,6 +36,10 @@ input:
type: file
description: |
path to VEP cache (optional)
- extra_files:
type: tuple
description: |
path to file(s) needed for plugins (optional)
output:
- vcf:
type: file

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@ -0,0 +1,42 @@
def VERSION = '0.3.14'
process HAPPY_HAPPY {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0':
'quay.io/biocontainers/hap.py:0.3.14--py27h5c5a3ab_0' }"
input:
tuple val(meta), path(truth_vcf), path(query_vcf), path(bed)
tuple path(fasta), path(fasta_fai)
output:
tuple val(meta), path('*.csv'), path('*.json') , emit: metrics
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}"
"""
hap.py \\
$truth_vcf \\
$query_vcf \\
$args \\
--reference $fasta \\
--threads $task.cpus \\
-R $bed \\
-o $prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
hap.py: $VERSION
END_VERSIONS
"""
}

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@ -0,0 +1,67 @@
name: "happy_happy"
description: Hap.py is a tool to compare diploid genotypes at haplotype level. Rather than comparing VCF records row by row, hap.py will generate and match alternate sequences in a superlocus. A superlocus is a small region of the genome (sized between 1 and around 1000 bp) that contains one or more variants.
keywords:
- happy
- benchmark
- haplotype
tools:
- "happy":
description: "Haplotype VCF comparison tools"
homepage: "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html"
documentation: "https://github.com/Illumina/hap.py"
tool_dev_url: "https://github.com/Illumina/hap.py"
doi: ""
licence: "['BSD-2-clause']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- truth_vcf:
type: file
description: gold standard VCF file
pattern: "*.{vcf,vcf.gz}"
- query_vcf:
type: file
description: VCF/GVCF file to query
pattern: "*.{vcf,vcf.gz}"
- bed:
type: file
description: BED file
pattern: "*.bed"
- fasta:
type: file
description: FASTA file of the reference genome
pattern: "*.{fa,fasta}"
- fasta_fai:
type: file
description: The index of the reference FASTA
pattern: "*.fai"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- summary:
type: file
description: A CSV file containing the summary of the benchmarking
pattern: "*.summary.csv"
- extended:
type: file
description: A CSV file containing extended info of the benchmarking
pattern: "*.extended.csv"
- runinfo:
type: file
description: A JSON file containing the run info
pattern: "*.runinfo.json"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@nvnieuwk"

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@ -0,0 +1,41 @@
def VERSION = '0.3.14'
process HAPPY_PREPY {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0':
'quay.io/biocontainers/hap.py:0.3.14--py27h5c5a3ab_0' }"
input:
tuple val(meta), path(vcf), path(bed)
tuple path(fasta), path(fasta_fai)
output:
tuple val(meta), path('*.vcf.gz') , emit: preprocessed_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}"
"""
pre.py \\
$args \\
-R $bed \\
--reference $fasta \\
--threads $task.cpus \\
$vcf \\
${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
pre.py: $VERSION
END_VERSIONS
"""
}

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@ -0,0 +1,55 @@
name: "happy_prepy"
description: Pre.py is a preprocessing tool made to preprocess VCF files for Hap.py
keywords:
- happy
- benchmark
- haplotype
tools:
- "happy":
description: "Haplotype VCF comparison tools"
homepage: "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html"
documentation: "https://github.com/Illumina/hap.py"
tool_dev_url: "https://github.com/Illumina/hap.py"
doi: ""
licence: "['BSD-2-clause']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: VCF file to preprocess
pattern: "*.{vcf,vcf.gz}"
- bed:
type: file
description: BED file
pattern: "*.bed"
- fasta:
type: file
description: FASTA file of the reference genome
pattern: "*.{fa,fasta}"
- fasta_fai:
type: file
description: The index of the reference FASTA
pattern: "*.fai"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: A preprocessed VCF file
pattern: "*.vcf.gz"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@nvnieuwk"

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@ -18,7 +18,9 @@ process KRONA_KRONADB {
script:
def args = task.ext.args ?: ''
"""
ktUpdateTaxonomy.sh taxonomy
ktUpdateTaxonomy.sh \\
$args \\
taxonomy/
cat <<-END_VERSIONS > versions.yml
"${task.process}":

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@ -23,7 +23,10 @@ process KRONA_KTIMPORTTAXONOMY {
script:
def args = task.ext.args ?: ''
"""
ktImportTaxonomy "$report" -tax taxonomy
ktImportTaxonomy \\
$args \\
-tax taxonomy/ \\
"$report"
cat <<-END_VERSIONS > versions.yml
"${task.process}":

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@ -23,8 +23,11 @@ input:
Groovy Map containing sample information
e.g. [ id:'test']
- database:
type: path
description: "Path to the taxonomy database downloaded by krona/kronadb"
type: file
description: |
Path to the taxonomy database .tab file downloaded by krona/ktUpdateTaxonomy
The file will be saved under a folder named "taxonomy" as "taxonomy/taxonomy.tab".
The parent folder will be passed as argument to ktImportTaxonomy.
- report:
type: file
description: "A tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes, and scores. Query IDs are taken from column 1, taxonomy IDs from column 2, and scores from column 3. Lines beginning with # will be ignored."

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@ -0,0 +1,30 @@
def VERSION='2.7.1' // Version information not provided by tool on CLI
process KRONA_KTUPDATETAXONOMY {
label 'process_low'
conda (params.enable_conda ? "bioconda::krona=2.7.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' :
'quay.io/biocontainers/krona:2.7.1--pl526_5' }"
output:
path 'taxonomy/taxonomy.tab', emit: db
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
ktUpdateTaxonomy.sh \\
$args \\
taxonomy/
cat <<-END_VERSIONS > versions.yml
"${task.process}":
krona: $VERSION
END_VERSIONS
"""
}

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@ -0,0 +1,31 @@
name: krona_ktupdatetaxonomy
description: KronaTools Update Taxonomy downloads a taxonomy database
keywords:
- database
- taxonomy
- krona
- visualisation
tools:
- krona:
description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
homepage: https://github.com/marbl/Krona/wiki/KronaTools
documentation: https://github.com/marbl/Krona/wiki/Installing
tool_dev_url:
doi: https://doi.org/10.1186/1471-2105-12-385
licence:
input:
- none: There is no input. This module downloads a pre-built taxonomy database for use with Krona Tools.
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- db:
type: file
description: A TAB separated file that contains a taxonomy database.
pattern: "*.{tab}"
authors:
- "@mjakobs"

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@ -0,0 +1,39 @@
process MOTUS_DOWNLOADDB {
label 'process_low'
conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
input:
path motus_downloaddb_script
output:
path "db_mOTU/" , emit: db
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def software = "${motus_downloaddb_script.simpleName}_copy.py"
"""
## must copy script file to working directory,
## otherwise the reference_db will be download to bin folder
## other than current directory
cp $motus_downloaddb_script ${software}
python ${software} \\
$args \\
-t $task.cpus
## mOTUs version number is not available from command line.
## mOTUs save the version number in index database folder.
## mOTUs will check the database version is same version as exec version.
cat <<-END_VERSIONS > versions.yml
"${task.process}":
mOTUs: \$(grep motus db_mOTU/db_mOTU_versions | sed 's/motus\\t//g')
END_VERSIONS
"""
}

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@ -0,0 +1,39 @@
name: "motus_downloaddb"
description: Download the mOTUs database
keywords:
- classify
- metagenomics
- fastq
- taxonomic profiling
- database
- download
tools:
- "motus":
description: "The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data."
homepage: "None"
documentation: "https://github.com/motu-tool/mOTUs/wiki"
tool_dev_url: "https://github.com/motu-tool/mOTUs"
doi: "10.1038/s41467-019-08844-4"
licence: "['GPL v3']"
input:
- motus_downloaddb:
type: directory
description: |
The mOTUs downloadDB script source file.
It is the source file installed or
remote source in github such as https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
pattern: "downloadDB.py"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- db:
type: directory
description: The mOTUs database directory
pattern: "db_mOTU"
authors:
- "@jianhong"

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@ -45,7 +45,7 @@ process SAMTOOLS_BAM2FQ {
bam2fq \\
$args \\
-@ $task.cpus \\
$inputbam >${prefix}_interleaved.fq.gz
$inputbam | gzip --no-name > ${prefix}_interleaved.fq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":

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@ -8,15 +8,16 @@ LABEL \
COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/nf-core-snpeff-5.0/bin:$PATH
# Setup default ARG variables
ARG GENOME=GRCh38
ARG SNPEFF_CACHE_VERSION=99
ARG SNPEFF_TAG=99
# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/nf-core-snpeff-${SNPEFF_TAG}/bin:$PATH
# Download Genome
RUN snpEff download -v ${GENOME}.${SNPEFF_CACHE_VERSION}
# Dump the details of the installed packages to a file for posterity
RUN conda env export --name nf-core-snpeff-5.0 > nf-core-snpeff-5.0.yml
RUN conda env export --name nf-core-snpeff-${SNPEFF_TAG} > nf-core-snpeff-${SNPEFF_TAG}.yml

5
modules/snpeff/build.sh Executable file → Normal file
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@ -9,10 +9,11 @@ build_push() {
SNPEFF_TAG=$3
docker build \
. \
-t nfcore/snpeff:${SNPEFF_TAG}.${GENOME} \
software/snpeff/. \
--build-arg GENOME=${GENOME} \
--build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION}
--build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION} \
--build-arg SNPEFF_TAG=${SNPEFF_TAG}
docker push nfcore/snpeff:${SNPEFF_TAG}.${GENOME}
}

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@ -10,18 +10,6 @@ tools:
homepage: https://pcingola.github.io/SnpEff/
documentation: https://pcingola.github.io/SnpEff/se_introduction/
licence: ["MIT"]
params:
- use_cache:
type: boolean
description: |
boolean to enable the usage of containers with cache
Enable the usage of containers with cache
Does not work with conda
- snpeff_tag:
type: value
description: |
Specify the tag for the container
https://hub.docker.com/r/nfcore/snpeff/tags
input:
- meta:
type: map

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@ -0,0 +1,31 @@
//
// Run VEP to annotate VCF files
//
include { ENSEMBLVEP } from '../../../../modules/ensemblvep/main'
include { TABIX_BGZIPTABIX } from '../../../../modules/tabix/bgziptabix/main'
workflow ANNOTATION_ENSEMBLVEP {
take:
vcf // channel: [ val(meta), vcf ]
vep_genome // value: genome to use
vep_species // value: species to use
vep_cache_version // value: cache version to use
vep_cache // path: /path/to/vep/cache (optionnal)
vep_extra_files // channel: [ file1, file2...] (optionnal)
main:
ch_versions = Channel.empty()
ENSEMBLVEP(vcf, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files)
TABIX_BGZIPTABIX(ENSEMBLVEP.out.vcf)
// Gather versions of all tools used
ch_versions = ch_versions.mix(ENSEMBLVEP.out.versions.first())
ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions.first())
emit:
vcf_tbi = TABIX_BGZIPTABIX.out.gz_tbi // channel: [ val(meta), vcf.gz, vcf.gz.tbi ]
reports = ENSEMBLVEP.out.report // path: *.html
versions = ch_versions // path: versions.yml
}

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@ -0,0 +1,49 @@
name: annotation_ensemblvep
description: |
Perform annotation with ensemblvep and bgzip + tabix index the resulting VCF file
keywords:
- ensemblvep
modules:
- ensemblvep
- tabix/bgziptabix
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: |
vcf to annotate
- genome:
type: value
description: |
which genome to annotate with
- species:
type: value
description: |
which species to annotate with
- cache_version:
type: value
description: |
which version of the cache to annotate with
- cache:
type: file
description: |
path to VEP cache (optional)
- extra_files:
type: tuple
description: |
path to file(s) needed for plugins (optional)
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- vcf_tbi:
type: file
description: Compressed vcf file + tabix index
pattern: "[ *{.vcf.gz,vcf.gz.tbi} ]"
authors:
- "@maxulysse"

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@ -0,0 +1,28 @@
//
// Run SNPEFF to annotate VCF files
//
include { SNPEFF } from '../../../../modules/snpeff/main'
include { TABIX_BGZIPTABIX } from '../../../../modules/tabix/bgziptabix/main'
workflow ANNOTATION_SNPEFF {
take:
vcf // channel: [ val(meta), vcf ]
snpeff_db // value: db version to use
snpeff_cache // path: /path/to/snpeff/cache (optionnal)
main:
ch_versions = Channel.empty()
SNPEFF(vcf, snpeff_db, snpeff_cache)
TABIX_BGZIPTABIX(SNPEFF.out.vcf)
// Gather versions of all tools used
ch_versions = ch_versions.mix(SNPEFF.out.versions.first())
ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions.first())
emit:
vcf_tbi = TABIX_BGZIPTABIX.out.gz_tbi // channel: [ val(meta), vcf.gz, vcf.gz.tbi ]
reports = SNPEFF.out.report // path: *.html
versions = ch_versions // path: versions.yml
}

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@ -11,11 +11,19 @@ input:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- input:
type: vcf
description: list containing one vcf file
pattern: "[ *.{vcf,vcf.gz} ]"
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: |
vcf to annotate
- db:
type: value
description: |
which db to annotate with
- cache:
type: file
description: |
path to snpEff cache (optional)
output:
- versions:
type: file

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@ -1,26 +0,0 @@
//
// Run VEP to annotate VCF files
//
include { ENSEMBLVEP } from '../../../modules/ensemblvep/main'
include { TABIX_BGZIPTABIX as ANNOTATION_BGZIPTABIX } from '../../../modules/tabix/bgziptabix/main'
workflow ANNOTATION_ENSEMBLVEP {
take:
vcf // channel: [ val(meta), vcf ]
vep_genome // value: which genome
vep_species // value: which species
vep_cache_version // value: which cache version
vep_cache // path: path_to_vep_cache (optionnal)
main:
ENSEMBLVEP(vcf, vep_genome, vep_species, vep_cache_version, vep_cache)
ANNOTATION_BGZIPTABIX(ENSEMBLVEP.out.vcf)
ch_versions = ENSEMBLVEP.out.versions.first().mix(ANNOTATION_BGZIPTABIX.out.versions.first())
emit:
vcf_tbi = ANNOTATION_BGZIPTABIX.out.gz_tbi // channel: [ val(meta), vcf.gz, vcf.gz.tbi ]
reports = ENSEMBLVEP.out.report // path: *.html
versions = ch_versions // path: versions.yml
}

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@ -1,29 +0,0 @@
name: annotation_ensemblvep
description: |
Perform annotation with ensemblvep and bgzip + tabix index the resulting VCF file
keywords:
- ensemblvep
modules:
- ensemblvep
- tabix/bgziptabix
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- input:
type: vcf
description: list containing one vcf file
pattern: "[ *.{vcf,vcf.gz} ]"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- vcf_tbi:
type: file
description: Compressed vcf file + tabix index
pattern: "[ *{.vcf.gz,vcf.gz.tbi} ]"
authors:
- "@maxulysse"

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@ -1,23 +0,0 @@
//
// Run SNPEFF to annotate VCF files
//
include { SNPEFF } from '../../../modules/snpeff/main'
include { TABIX_BGZIPTABIX as ANNOTATION_BGZIPTABIX } from '../../../modules/tabix/bgziptabix/main'
workflow ANNOTATION_SNPEFF {
take:
vcf // channel: [ val(meta), vcf ]
snpeff_db // value: version of db to use
snpeff_cache // path: path_to_snpeff_cache (optionnal)
main:
SNPEFF(vcf, snpeff_db, snpeff_cache)
ANNOTATION_BGZIPTABIX(SNPEFF.out.vcf)
ch_versions = SNPEFF.out.versions.first().mix(ANNOTATION_BGZIPTABIX.out.versions.first())
emit:
vcf_tbi = ANNOTATION_BGZIPTABIX.out.gz_tbi // channel: [ val(meta), vcf.gz, vcf.gz.tbi ]
reports = SNPEFF.out.report // path: *.html
versions = ch_versions // path: versions.yml
}

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@ -891,6 +891,14 @@ hamronization/summarize:
- modules/hamronization/summarize/**
- tests/modules/hamronization/summarize/**
happy/happy:
- modules/happy/happy/**
- tests/modules/happy/happy/**
happy/prepy:
- modules/happy/prepy/**
- tests/modules/happy/prepy/**
hicap:
- modules/hicap/**
- tests/modules/hicap/**
@ -1050,6 +1058,10 @@ krona/kronadb:
- modules/krona/kronadb/**
- tests/modules/krona/kronadb/**
krona/ktupdatetaxonomy:
- modules/krona/ktupdatetaxonomy/**
- tests/modules/krona/ktupdatetaxonomy/**
krona/ktimporttaxonomy:
- modules/krona/ktimporttaxonomy/**
- tests/modules/krona/ktimporttaxonomy/**
@ -1242,6 +1254,10 @@ mosdepth:
- modules/mosdepth/**
- tests/modules/mosdepth/**
motus/downloaddb:
- modules/motus/downloaddb/**
- tests/modules/motus/downloaddb/**
msisensor/msi:
- modules/msisensor/msi/**
- tests/modules/msisensor/msi/**

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@ -111,7 +111,9 @@ params {
test_sequencing_summary = "${test_data_dir}/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt"
}
'metagenome' {
classified_reads_assignment = "${test_data_dir}/genomics/sarscov2/metagenome/test_1.kraken2.reads.txt"
kraken_report = "${test_data_dir}/genomics/sarscov2/metagenome/test_1.kraken2.report.txt"
krona_taxonomy = "${test_data_dir}/genomics/sarscov2/metagenome/krona_taxonomy.tab"
}
}
'homo_sapiens' {

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@ -10,5 +10,5 @@ workflow test_ensemblvep {
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
]
ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [] )
ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], [] )
}

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@ -0,0 +1,39 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { HAPPY_HAPPY } from '../../../../modules/happy/happy/main.nf'
workflow test_happy_vcf {
input = [
[ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
]
fasta = Channel.value([
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
])
HAPPY_HAPPY ( input, fasta )
}
workflow test_happy_gvcf {
input = [
[ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
]
fasta = Channel.value([
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
])
HAPPY_HAPPY ( input, fasta )
}

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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 +1,27 @@
- name: happy happy test_happy_vcf
command: nextflow run tests/modules/happy/happy -entry test_happy_vcf -c tests/config/nextflow.config
tags:
- happy
- happy/happy
files:
- path: output/happy/test.extended.csv
md5sum: ef79c7c789ef4f146ca2e50dafaf22b3
- path: output/happy/test.runinfo.json
- path: output/happy/test.summary.csv
md5sum: f8aa5d36d3c48dede2f607fd565894ad
- path: output/happy/versions.yml
md5sum: 82243bf6dbdc71aa63211ee2a89f47f2
- name: happy happy test_happy_gvcf
command: nextflow run tests/modules/happy/happy -entry test_happy_gvcf -c tests/config/nextflow.config
tags:
- happy
- happy/happy
files:
- path: output/happy/test.extended.csv
md5sum: 3d5c21b67a259a3f6dcb088d55b86cd3
- path: output/happy/test.runinfo.json
- path: output/happy/test.summary.csv
md5sum: 03044e9bb5a0c6f0947b7e910fc8a558
- path: output/happy/versions.yml
md5sum: 551fa216952d6f5de78e6e453b92aaab

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@ -0,0 +1,37 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { HAPPY_PREPY } from '../../../../modules/happy/prepy/main.nf'
workflow test_happy_prepy_vcf {
input = [
[ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
]
fasta = Channel.value([
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
])
HAPPY_PREPY ( input, fasta )
}
workflow test_happy_prepy_gvcf {
input = [
[ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
]
fasta = Channel.value([
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
])
HAPPY_PREPY ( input, fasta )
}

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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 +1,19 @@
- name: happy prepy test_happy_prepy_vcf
command: nextflow run tests/modules/happy/prepy -entry test_happy_prepy_vcf -c tests/config/nextflow.config
tags:
- happy/prepy
- happy
files:
- path: output/happy/test.vcf.gz
- path: output/happy/versions.yml
md5sum: 814d20f1f29f23a3d21012748a5d6393
- name: happy prepy test_happy_prepy_gvcf
command: nextflow run tests/modules/happy/prepy -entry test_happy_prepy_gvcf -c tests/config/nextflow.config
tags:
- happy/prepy
- happy
files:
- path: output/happy/test.vcf.gz
- path: output/happy/versions.yml
md5sum: 970a54de46e68ef6d5228a26eaa4c8e7

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@ -2,15 +2,27 @@
nextflow.enable.dsl = 2
include { KRONA_KTIMPORTTAXONOMY } from '../../../../modules/krona/ktimporttaxonomy/main.nf'
include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_READS } from '../../../../modules/krona/ktimporttaxonomy/main.nf'
include { KRONA_KTIMPORTTAXONOMY as KRONA_KTIMPORTTAXONOMY_REPORT } from '../../../../modules/krona/ktimporttaxonomy/main.nf'
workflow test_krona_ktimporttaxonomy {
workflow test_krona_ktimporttaxonomy_reads {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
file(params.test_data['sarscov2']['metagenome']['classified_reads_assignment'], checkIfExists: true)
]
taxonomy = file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
taxonomy = file(params.test_data['sarscov2']['metagenome']['krona_taxonomy'], checkIfExists: true)
KRONA_KTIMPORTTAXONOMY ( input, taxonomy )
KRONA_KTIMPORTTAXONOMY_READS ( input, taxonomy )
}
workflow test_krona_ktimporttaxonomy_report {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['metagenome']['kraken_report'], checkIfExists: true)
]
taxonomy = file(params.test_data['sarscov2']['metagenome']['krona_taxonomy'], checkIfExists: true)
KRONA_KTIMPORTTAXONOMY_REPORT ( input, taxonomy )
}

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@ -2,4 +2,12 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: KRONA_KTIMPORTTAXONOMY_READS {
ext.args = '-t 3'
}
withName: KRONA_KTIMPORTTAXONOMY_REPORT {
ext.args = '-m 3 -t 5'
}
}

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@ -1,9 +1,23 @@
- name: krona ktimporttaxonomy test_krona_ktimporttaxonomy
command: nextflow run ./tests/modules/krona/ktimporttaxonomy -entry test_krona_ktimporttaxonomy -c ./tests/config/nextflow.config -c ./tests/modules/krona/ktimporttaxonomy/nextflow.config
- name: krona ktimporttaxonomy test_krona_ktimporttaxonomy_reads
command: nextflow run tests/modules/krona/ktimporttaxonomy -entry test_krona_ktimporttaxonomy_reads -c tests/config/nextflow.config
tags:
- krona/ktimporttaxonomy
- krona
- krona/ktimporttaxonomy
files:
- path: output/krona/taxonomy.krona.html
contains:
- "DOCTYPE html PUBLIC"
- path: output/krona/versions.yml
md5sum: 660a8c151191bf4c63bd96db2c7fe503
- name: krona ktimporttaxonomy test_krona_ktimporttaxonomy_report
command: nextflow run tests/modules/krona/ktimporttaxonomy -entry test_krona_ktimporttaxonomy_report -c tests/config/nextflow.config
tags:
- krona
- krona/ktimporttaxonomy
files:
- path: output/krona/taxonomy.krona.html
contains:
- "DOCTYPE html PUBLIC"
- path: output/krona/versions.yml
md5sum: 8a593c16bb2d4132638fb0fc342fe2b7

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@ -0,0 +1,9 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { KRONA_KTUPDATETAXONOMY } from '../../../../modules/krona/ktupdatetaxonomy/main.nf'
workflow test_krona_ktupdatetaxonomy {
KRONA_KTUPDATETAXONOMY ( )
}

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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 +1,7 @@
- name: krona ktupdatetaxonomy test_krona_ktupdatetaxonomy
command: nextflow run ./tests/modules/krona/ktupdatetaxonomy -entry test_krona_ktupdatetaxonomy -c ./tests/config/nextflow.config -c ./tests/modules/krona/ktupdatetaxonomy/nextflow.config
tags:
- krona
- krona/ktupdatetaxonomy
files:
- path: output/krona/taxonomy/taxonomy.tab

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@ -0,0 +1,12 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { MOTUS_DOWNLOADDB } from '../../../../modules/motus/downloaddb/main.nf'
workflow test_motus_downloaddb {
input = file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py')
MOTUS_DOWNLOADDB ( input )
}

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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 +1,7 @@
- name: motus downloaddb test_motus_downloaddb
command: nextflow run tests/modules/motus/downloaddb -entry test_motus_downloaddb -c tests/config/nextflow.config
tags:
- motus
- motus/downloaddb
files:
- path: output/motus/db_mOTU/db_mOTU_versions

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@ -1,14 +1,15 @@
- name: samtools bam2fq test_samtools_bam2fq_nosplit
command: nextflow run ./tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_nosplit -c ./tests/config/nextflow.config -c ./tests/modules/samtools/bam2fq/nextflow.config
command: nextflow run tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_nosplit -c tests/config/nextflow.config
tags:
- samtools/bam2fq
- samtools
files:
- path: output/samtools/test_interleaved.fq.gz
md5sum: d733e66d29a4b366bf9df8c42f845256
- path: output/samtools/versions.yml
md5sum: 4973eac1b6a8f090d5fcd4456d65a894
- name: samtools bam2fq test_samtools_bam2fq_withsplit
command: nextflow run ./tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_withsplit -c ./tests/config/nextflow.config -c ./tests/modules/samtools/bam2fq/nextflow.config
command: nextflow run tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_withsplit -c tests/config/nextflow.config
tags:
- samtools/bam2fq
- samtools
@ -21,3 +22,5 @@
md5sum: 709872fc2910431b1e8b7074bfe38c67
- path: output/samtools/test_singleton.fq.gz
md5sum: 709872fc2910431b1e8b7074bfe38c67
- path: output/samtools/versions.yml
md5sum: e92d21bbcda2fed7cb438d95c51edff0

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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { ANNOTATION_ENSEMBLVEP } from '../../../../subworkflows/nf-core/annotation_ensemblvep/main'
include { ANNOTATION_ENSEMBLVEP } from '../../../../../subworkflows/nf-core/annotation/ensemblvep/main'
workflow annotation_ensemblvep {
input = [
@ -10,5 +10,5 @@ workflow annotation_ensemblvep {
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
]
ANNOTATION_ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [] )
ANNOTATION_ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], [] )
}

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@ -7,7 +7,7 @@ process {
publishDir = [ enabled: false ]
}
withName: ANNOTATION_BGZIPTABIX {
withName: TABIX_BGZIPTABIX {
ext.prefix = { "${meta.id}_VEP.ann.vcf" }
}

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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
include { ANNOTATION_SNPEFF } from '../../../../subworkflows/nf-core/annotation_snpeff/main'
include { ANNOTATION_SNPEFF } from '../../../../../subworkflows/nf-core/annotation_snpeff/main'
workflow annotation_snpeff {
input = [

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@ -7,7 +7,7 @@ process {
publishDir = [ enabled: false ]
}
withName: ANNOTATION_BGZIPTABIX {
withName: TABIX_BGZIPTABIX {
ext.prefix = { "${meta.id}_snpEff.ann.vcf" }
}