Merge remote-tracking branch 'origin' into motus_profile
JIANHONG OU
2 years ago
parent
0f24e4dcff
commit
c8f2c44e22
@ -1,64 +0,0 @@
|
||||
---
|
||||
name: Bug report
|
||||
about: Report something that is broken or incorrect
|
||||
title: "[BUG]"
|
||||
---
|
||||
|
||||
<!--
|
||||
# nf-core/module bug report
|
||||
|
||||
Hi there!
|
||||
|
||||
Thanks for telling us about a problem with the modules.
|
||||
Please delete this text and anything that's not relevant from the template below:
|
||||
-->
|
||||
|
||||
## Check Documentation
|
||||
|
||||
I have checked the following places for your error:
|
||||
|
||||
- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
|
||||
- [ ] [nf-core/module documentation](https://github.com/nf-core/modules/blob/master/README.md)
|
||||
|
||||
## Description of the bug
|
||||
|
||||
<!-- A clear and concise description of what the bug is. -->
|
||||
|
||||
## Steps to reproduce
|
||||
|
||||
Steps to reproduce the behaviour:
|
||||
|
||||
1. Command line: <!-- [e.g. `nextflow run ...`] -->
|
||||
2. See error: <!-- [Please provide your error message] -->
|
||||
|
||||
## Expected behaviour
|
||||
|
||||
<!-- A clear and concise description of what you expected to happen. -->
|
||||
|
||||
## Log files
|
||||
|
||||
Have you provided the following extra information/files:
|
||||
|
||||
- [ ] The command used to run the module
|
||||
- [ ] The `.nextflow.log` file <!-- this is a hidden file in the directory where you launched the module -->
|
||||
|
||||
## System
|
||||
|
||||
- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
|
||||
- Executor: <!-- [e.g. slurm, local, awsbatch...] -->
|
||||
- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
|
||||
- Version <!-- [e.g. 7, 10.13.6, 18.3...] -->
|
||||
|
||||
## Nextflow Installation
|
||||
|
||||
- Version: <!-- [e.g. 19.10.0] -->
|
||||
|
||||
## Container engine
|
||||
|
||||
- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
|
||||
- version: <!-- [e.g. 1.0.0] -->
|
||||
- Image tag: <!-- [e.g. nfcore/module:2.6] -->
|
||||
|
||||
## Additional context
|
||||
|
||||
<!-- Add any other context about the problem here. -->
|
||||
@ -0,0 +1,52 @@
|
||||
name: Bug report
|
||||
description: Report something that is broken or incorrect
|
||||
labels: bug
|
||||
body:
|
||||
- type: checkboxes
|
||||
attributes:
|
||||
label: Have you checked the docs?
|
||||
description: I have checked the following places for my error
|
||||
options:
|
||||
- label: "[nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)"
|
||||
required: true
|
||||
- label: "[nf-core modules documentation](https://nf-co.re/docs/contributing/modules)"
|
||||
required: true
|
||||
|
||||
- type: textarea
|
||||
id: description
|
||||
attributes:
|
||||
label: Description of the bug
|
||||
description: A clear and concise description of what the bug is.
|
||||
validations:
|
||||
required: true
|
||||
|
||||
- type: textarea
|
||||
id: command_used
|
||||
attributes:
|
||||
label: Command used and terminal output
|
||||
description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
|
||||
render: console
|
||||
placeholder: |
|
||||
$ nextflow run ...
|
||||
|
||||
Some output where something broke
|
||||
|
||||
- type: textarea
|
||||
id: files
|
||||
attributes:
|
||||
label: Relevant files
|
||||
description: |
|
||||
Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
|
||||
Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
|
||||
|
||||
- type: textarea
|
||||
id: system
|
||||
attributes:
|
||||
label: System information
|
||||
description: |
|
||||
* Nextflow version _(eg. 21.10.3)_
|
||||
* Hardware _(eg. HPC, Desktop, Cloud)_
|
||||
* Executor _(eg. slurm, local, awsbatch)_
|
||||
* Container engine and version: _(e.g. Docker 1.0.0, Singularity, Conda, Podman, Shifter or Charliecloud)_
|
||||
* OS and version: _(eg. CentOS Linux, macOS, Ubuntu 22.04)_
|
||||
* Image tag: <!-- [e.g. nfcore/cellranger:2.6] -->
|
||||
@ -1,32 +0,0 @@
|
||||
---
|
||||
name: Feature request
|
||||
about: Suggest an idea for nf-core/modules
|
||||
title: "[FEATURE]"
|
||||
---
|
||||
|
||||
<!--
|
||||
# nf-core/modules feature request
|
||||
|
||||
Hi there!
|
||||
|
||||
Thanks for suggesting a new feature for the modules!
|
||||
Please delete this text and anything that's not relevant from the template below:
|
||||
-->
|
||||
|
||||
## Is your feature request related to a problem? Please describe
|
||||
|
||||
<!-- A clear and concise description of what the problem is. -->
|
||||
|
||||
<!-- e.g. [I'm always frustrated when ...] -->
|
||||
|
||||
## Describe the solution you'd like
|
||||
|
||||
<!-- A clear and concise description of what you want to happen. -->
|
||||
|
||||
## Describe alternatives you've considered
|
||||
|
||||
<!-- A clear and concise description of any alternative solutions or features you've considered. -->
|
||||
|
||||
## Additional context
|
||||
|
||||
<!-- Add any other context about the feature request here. -->
|
||||
@ -0,0 +1,32 @@
|
||||
name: Feature request
|
||||
description: Suggest an idea for nf-core/modules
|
||||
labels: feature
|
||||
title: "[FEATURE]"
|
||||
body:
|
||||
- type: textarea
|
||||
id: description
|
||||
attributes:
|
||||
label: Is your feature request related to a problem? Please describe
|
||||
description: A clear and concise description of what the bug is.
|
||||
placeholder: |
|
||||
<!-- e.g. [I'm always frustrated when ...] -->
|
||||
validations:
|
||||
required: true
|
||||
|
||||
- type: textarea
|
||||
id: solution
|
||||
attributes:
|
||||
label: Describe the solution you'd like
|
||||
description: A clear and concise description of the solution you want to happen.
|
||||
|
||||
- type: textarea
|
||||
id: alternatives
|
||||
attributes:
|
||||
label: Describe alternatives you've considered
|
||||
description: A clear and concise description of any alternative solutions or features you've considered.
|
||||
|
||||
- type: textarea
|
||||
id: additional_context
|
||||
attributes:
|
||||
label: Additional context
|
||||
description: Add any other context about the feature request here.
|
||||
@ -1,26 +0,0 @@
|
||||
---
|
||||
name: New module
|
||||
about: Suggest a new module for nf-core/modules
|
||||
title: "new module: TOOL/SUBTOOL"
|
||||
label: new module
|
||||
---
|
||||
|
||||
<!--
|
||||
# nf-core/modules new module suggestion
|
||||
|
||||
Hi there!
|
||||
|
||||
Thanks for suggesting a new module for the modules!
|
||||
Please delete this text and anything that's not relevant from the template below:
|
||||
|
||||
Replace TOOL with the bioconda name for the tool in the following text, so that the link is functional.
|
||||
|
||||
Replace TOOL/SUBTOOL in the issue title so that it's understandable.
|
||||
-->
|
||||
|
||||
I think it would be good to have a module for [TOOL](https://bioconda.github.io/recipes/TOOL/README.html)
|
||||
|
||||
- [ ] This module does not exist yet with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command
|
||||
- [ ] There is no [open pull request](https://github.com/nf-core/modules/pulls) for this module
|
||||
- [ ] There is no [open issue](https://github.com/nf-core/modules/issues) for this module
|
||||
- [ ] If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module
|
||||
@ -0,0 +1,36 @@
|
||||
name: New module
|
||||
description: Suggest a new module for nf-core/modules
|
||||
title: "new module: TOOL/SUBTOOL"
|
||||
labels: new module
|
||||
body:
|
||||
- type: checkboxes
|
||||
attributes:
|
||||
label: Is there an existing module for this?
|
||||
description: This module does not exist yet with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command
|
||||
options:
|
||||
- label: I have searched for the existing module
|
||||
required: true
|
||||
|
||||
- type: checkboxes
|
||||
attributes:
|
||||
label: Is there an open PR for this?
|
||||
description: There is no [open pull request](https://github.com/nf-core/modules/pulls) for this module
|
||||
options:
|
||||
- label: I have searched for existing PRs
|
||||
required: true
|
||||
|
||||
- type: checkboxes
|
||||
attributes:
|
||||
label: Is there an open issue for this?
|
||||
description: There is no [open issue](https://github.com/nf-core/modules/issues) for this module
|
||||
options:
|
||||
- label: I have searched for existing issues
|
||||
required: true
|
||||
|
||||
- type: checkboxes
|
||||
attributes:
|
||||
label: Are you going to work on this?
|
||||
description: If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module
|
||||
options:
|
||||
- label: If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module
|
||||
required: false
|
||||
@ -0,0 +1,43 @@
|
||||
process ELPREP_MERGE {
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||||
tag "$meta.id"
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||||
label 'process_low'
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||||
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conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0':
|
||||
'quay.io/biocontainers/elprep:5.1.2--he881be0_0' }"
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|
||||
input:
|
||||
tuple val(meta), path(bam)
|
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|
||||
output:
|
||||
tuple val(meta), path("output/**.{bam,sam}") , emit: bam
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||||
path "versions.yml" , emit: versions
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||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
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||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def suffix = args.contains("--output-type sam") ? "sam" : "bam"
|
||||
def single_end = meta.single_end ? " --single-end" : ""
|
||||
|
||||
"""
|
||||
# create directory and move all input so elprep can find and merge them before splitting
|
||||
mkdir input
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||||
mv ${bam} input/
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||||
|
||||
elprep merge \\
|
||||
input/ \\
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||||
output/${prefix}.${suffix} \\
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||||
$args \\
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||||
${single_end} \\
|
||||
--nr-of-threads $task.cpus
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
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@ -0,0 +1,44 @@
|
||||
name: "elprep_merge"
|
||||
description: Merge split bam/sam chunks in one file
|
||||
keywords:
|
||||
- bam
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||||
- sam
|
||||
- merge
|
||||
tools:
|
||||
- "elprep":
|
||||
description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4."
|
||||
homepage: "https://github.com/ExaScience/elprep"
|
||||
documentation: "https://github.com/ExaScience/elprep"
|
||||
tool_dev_url: "https://github.com/ExaScience/elprep"
|
||||
doi: "10.1371/journal.pone.0244471"
|
||||
licence: "['AGPL v3']"
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: List of BAM/SAM chunks to merge
|
||||
pattern: "*.{bam,sam}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
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description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
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#
|
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- versions:
|
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type: file
|
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description: File containing software versions
|
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pattern: "versions.yml"
|
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- bam:
|
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type: file
|
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description: Merged BAM/SAM file
|
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pattern: "*.{bam,sam}"
|
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|
||||
authors:
|
||||
- "@matthdsm"
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@ -0,0 +1,42 @@
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def VERSION = '0.3.14'
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process HAPPY_HAPPY {
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tag "$meta.id"
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label 'process_medium'
|
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|
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conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null)
|
||||
container "${ 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' }"
|
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|
||||
input:
|
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tuple val(meta), path(truth_vcf), path(query_vcf), path(bed)
|
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tuple path(fasta), path(fasta_fai)
|
||||
|
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output:
|
||||
tuple val(meta), path('*.csv'), path('*.json') , emit: metrics
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||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
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task.ext.when == null || task.ext.when
|
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script:
|
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def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
||||
"""
|
||||
hap.py \\
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$truth_vcf \\
|
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$query_vcf \\
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||||
$args \\
|
||||
--reference $fasta \\
|
||||
--threads $task.cpus \\
|
||||
-R $bed \\
|
||||
-o $prefix
|
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|
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
|
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hap.py: $VERSION
|
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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.
|
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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"
|
||||
@ -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: $VERSION
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,55 @@
|
||||
name: "happy_prepy"
|
||||
description: Pre.py is a preprocessing tool made to preprocess VCF files for Hap.py
|
||||
keywords:
|
||||
- happy
|
||||
- benchmark
|
||||
- haplotype
|
||||
tools:
|
||||
- "happy":
|
||||
description: "Haplotype VCF comparison tools"
|
||||
homepage: "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html"
|
||||
documentation: "https://github.com/Illumina/hap.py"
|
||||
tool_dev_url: "https://github.com/Illumina/hap.py"
|
||||
doi: ""
|
||||
licence: "['BSD-2-clause']"
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF file to preprocess
|
||||
pattern: "*.{vcf,vcf.gz}"
|
||||
- bed:
|
||||
type: file
|
||||
description: BED file
|
||||
pattern: "*.bed"
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA file of the reference genome
|
||||
pattern: "*.{fa,fasta}"
|
||||
- fasta_fai:
|
||||
type: file
|
||||
description: The index of the reference FASTA
|
||||
pattern: "*.fai"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: A preprocessed VCF file
|
||||
pattern: "*.vcf.gz"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
|
||||
authors:
|
||||
- "@nvnieuwk"
|
||||
@ -0,0 +1,34 @@
|
||||
process KRONA_KTIMPORTTEXT {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::krona=2.8.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1':
|
||||
'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(report)
|
||||
|
||||
output:
|
||||
tuple val(meta), path ('*.html'), emit: html
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
ktImportText \\
|
||||
$args \\
|
||||
-o ${prefix}.html \\
|
||||
$report
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
krona: \$( echo \$(ktImportText 2>&1) | sed 's/^.*KronaTools //g; s/- ktImportText.*\$//g')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,47 @@
|
||||
name: "krona_ktimporttext"
|
||||
description: Creates a Krona chart from text files listing quantities and lineages.
|
||||
keywords:
|
||||
- plot
|
||||
- taxonomy
|
||||
- interactive
|
||||
- html
|
||||
- visualisation
|
||||
- krona chart
|
||||
- metagenomics
|
||||
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: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html
|
||||
tool_dev_url: https://github.com/marbl/Krona
|
||||
doi: 10.1186/1471-2105-12-385
|
||||
licence: https://raw.githubusercontent.com/marbl/Krona/master/KronaTools/LICENSE.txt
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test']
|
||||
- report:
|
||||
type: file
|
||||
description: "Tab-delimited text file. Each line should be a number followed by a list of wedges to contribute to (starting from the highest level). If no wedges are listed (and just a quantity is given), it will contribute to the top level. If the same lineage is listed more than once, the values will be added. Quantities can be omitted if -q is specified. Lines beginning with '#' will be ignored."
|
||||
pattern: "*.{txt}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test' ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- html:
|
||||
type: file
|
||||
description: A html file containing an interactive krona plot.
|
||||
pattern: "*.{html}"
|
||||
|
||||
authors:
|
||||
- "@jianhong"
|
||||
@ -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: $VERSION
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,31 @@
|
||||
name: krona_ktupdatetaxonomy
|
||||
description: KronaTools Update Taxonomy downloads a taxonomy database
|
||||
keywords:
|
||||
- database
|
||||
- taxonomy
|
||||
- krona
|
||||
- visualisation
|
||||
tools:
|
||||
- krona:
|
||||
description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
|
||||
homepage: https://github.com/marbl/Krona/wiki/KronaTools
|
||||
documentation: https://github.com/marbl/Krona/wiki/Installing
|
||||
tool_dev_url:
|
||||
doi: https://doi.org/10.1186/1471-2105-12-385
|
||||
licence:
|
||||
|
||||
input:
|
||||
- none: There is no input. This module downloads a pre-built taxonomy database for use with Krona Tools.
|
||||
|
||||
output:
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- db:
|
||||
type: file
|
||||
description: A TAB separated file that contains a taxonomy database.
|
||||
pattern: "*.{tab}"
|
||||
|
||||
authors:
|
||||
- "@mjakobs"
|
||||
@ -0,0 +1,39 @@
|
||||
process MOTUS_DOWNLOADDB {
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
|
||||
container "${ 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
|
||||
"""
|
||||
}
|
||||
@ -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"
|
||||
@ -0,0 +1,64 @@
|
||||
process SHIGATYPER {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::shigatyper=2.0.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/shigatyper%3A2.0.1--pyhdfd78af_0':
|
||||
'quay.io/biocontainers/shigatyper:2.0.1--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("${prefix}.tsv") , emit: tsv
|
||||
tuple val(meta), path("${prefix}-hits.tsv"), optional: true, emit: hits
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
||||
if (meta.is_ont) {
|
||||
"""
|
||||
shigatyper \\
|
||||
$args \\
|
||||
--SE $reads \\
|
||||
--ont \\
|
||||
--name $prefix
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
shigatyper: \$(echo \$(shigatyper --version 2>&1) | sed 's/^.*ShigaTyper //' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else if (meta.single_end) {
|
||||
"""
|
||||
shigatyper \\
|
||||
$args \\
|
||||
--SE $reads \\
|
||||
--name $prefix
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
shigatyper: \$(echo \$(shigatyper --version 2>&1) | sed 's/^.*ShigaTyper //' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
shigatyper \\
|
||||
$args \\
|
||||
--R1 ${reads[0]} \\
|
||||
--R2 ${reads[1]} \\
|
||||
--name $prefix
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
shigatyper: \$(echo \$(shigatyper --version 2>&1) | sed 's/^.*ShigaTyper //' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,47 @@
|
||||
name: "shigatyper"
|
||||
description: Determine Shigella serotype from Illumina or Oxford Nanopore reads
|
||||
keywords:
|
||||
- fastq
|
||||
- shigella
|
||||
- serotype
|
||||
tools:
|
||||
- "shigatyper":
|
||||
description: "Typing tool for Shigella spp. from WGS Illumina sequencing"
|
||||
homepage: "https://github.com/CFSAN-Biostatistics/shigatyper"
|
||||
documentation: "https://github.com/CFSAN-Biostatistics/shigatyper"
|
||||
tool_dev_url: "https://github.com/CFSAN-Biostatistics/shigatyper"
|
||||
doi: "10.1128/AEM.00165-19"
|
||||
licence: "['Public Domain']"
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false, is_ont:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: Illumina or Nanopore FASTQ file
|
||||
pattern: "*.fastq.gz"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- tsv:
|
||||
type: file
|
||||
description: A TSV formatted file with ShigaTyper results
|
||||
pattern: "*.tsv"
|
||||
- hits:
|
||||
type: file
|
||||
description: A TSV formatted file with individual gene hits
|
||||
pattern: "*-hits.tsv"
|
||||
|
||||
authors:
|
||||
- "@rpetit3"
|
||||
@ -0,0 +1,52 @@
|
||||
def VERSION = '2.04'
|
||||
|
||||
process SLIMFASTQ {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::slimfastq=2.04" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/slimfastq:2.04--h87f3376_2':
|
||||
'quay.io/biocontainers/slimfastq:2.04--h87f3376_2' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fastq)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.sfq"), emit: sfq
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
if (meta.single_end) {
|
||||
"""
|
||||
gzip -d -c '${fastq}' | slimfastq \\
|
||||
$args \\
|
||||
-f '${prefix}.sfq'
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
slimfastq: ${VERSION}
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
gzip -d -c '${fastq[0]}' | slimfastq \\
|
||||
$args \\
|
||||
-f '${prefix}_1.sfq'
|
||||
|
||||
gzip -d -c '${fastq[1]}' | slimfastq \\
|
||||
$args \\
|
||||
-f '${prefix}_2.sfq'
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
slimfastq: ${VERSION}
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,41 @@
|
||||
name: "slimfastq"
|
||||
description: Fast, efficient, lossless compression of FASTQ files.
|
||||
keywords:
|
||||
- FASTQ
|
||||
- compression
|
||||
- lossless
|
||||
tools:
|
||||
- "slimfastq":
|
||||
description: "slimfastq efficiently compresses/decompresses FASTQ files"
|
||||
homepage: "https://github.com/Infinidat/slimfastq"
|
||||
tool_dev_url: "https://github.com/Infinidat/slimfastq"
|
||||
licence: "['BSD-3-clause']"
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fastq:
|
||||
type: file
|
||||
description: Either a single-end FASTQ file or paired-end files.
|
||||
pattern: "*.{fq.gz,fastq.gz}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- sfq:
|
||||
type: file
|
||||
description: Either one or two sequence files in slimfastq compressed format.
|
||||
pattern: "*.{sfq}"
|
||||
|
||||
authors:
|
||||
- "@Midnighter"
|
||||
@ -0,0 +1,47 @@
|
||||
process SRST2_SRST2 {
|
||||
tag "${meta.id}"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::srst2=0.2.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/srst2%3A0.2.0--py27_2':
|
||||
'quay.io/biocontainers/srst2:0.2.0--py27_2'}"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fastq_s), path(db)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*_genes_*_results.txt") , optional:true, emit: gene_results
|
||||
tuple val(meta), path("*_fullgenes_*_results.txt") , optional:true, emit: fullgene_results
|
||||
tuple val(meta), path("*_mlst_*_results.txt") , optional:true, emit: mlst_results
|
||||
tuple val(meta), path("*.pileup") , emit: pileup
|
||||
tuple val(meta), path("*.sorted.bam") , emit: sorted_bam
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ""
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def read_s = meta.single_end ? "--input_se ${fastq_s}" : "--input_pe ${fastq_s[0]} ${fastq_s[1]}"
|
||||
if (meta.db=="gene") {
|
||||
database = "--gene_db ${db}"
|
||||
} else if (meta.db=="mlst") {
|
||||
database = "--mlst_db ${db}"
|
||||
} else {
|
||||
error "Please set meta.db to either \"gene\" or \"mlst\""
|
||||
}
|
||||
"""
|
||||
srst2 \\
|
||||
${read_s} \\
|
||||
--threads $task.cpus \\
|
||||
--output ${prefix} \\
|
||||
${database} \\
|
||||
$args
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
srst2: \$(echo \$(srst2 --version 2>&1) | sed 's/srst2 //' ))
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,72 @@
|
||||
name: srst2_srst2
|
||||
description: |
|
||||
Short Read Sequence Typing for Bacterial Pathogens is a program designed to take Illumina sequence data,
|
||||
a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc)
|
||||
and report the presence of STs and/or reference genes.
|
||||
keywords:
|
||||
- mlst
|
||||
- typing
|
||||
- illumina
|
||||
tools:
|
||||
- srst2:
|
||||
description: "Short Read Sequence Typing for Bacterial Pathogens"
|
||||
homepage: "http://katholt.github.io/srst2/"
|
||||
documentation: "https://github.com/katholt/srst2/blob/master/README.md"
|
||||
tool_dev_url: "https://github.com/katholt/srst2"
|
||||
doi: "10.1186/s13073-014-0090-6"
|
||||
licence: ["BSD"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map0.2.0-4
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
id: should be the identification number or sample name
|
||||
single_end: should be true for single end data and false for paired in data
|
||||
db: should be either 'gene' to use the --gene_db option or "mlst" to use the --mlst_db option
|
||||
e.g. [ id:'sample', single_end:false , db:'gene']
|
||||
- fasta:
|
||||
type: file
|
||||
description: |
|
||||
gzipped fasta file. If files are NOT in
|
||||
MiSeq format sample_S1_L001_R1_001.fastq.gz uses --forward and --reverse parameters; otherwise
|
||||
default is _1, i.e. expect forward reads as sample_1.fastq.gz).
|
||||
pattern: "*.fastq.gz"
|
||||
- db:
|
||||
type: file
|
||||
description: Database in FASTA format
|
||||
pattern: "*.fasta"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'sample', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- txt:
|
||||
type: file
|
||||
description: A detailed report, with one row per gene per sample described here github.com/katholt/srst2#gene-typing
|
||||
pattern: "*_fullgenes_*_results.txt"
|
||||
- txt:
|
||||
type: file
|
||||
description: A tabulated summary report of samples x genes.
|
||||
pattern: "*_genes_*_results.txt"
|
||||
- txt:
|
||||
type: file
|
||||
description: A tabulated summary report of mlst subtyping.
|
||||
pattern: "*_mlst_*_results.txt"
|
||||
- bam:
|
||||
type: file
|
||||
description: Sorted BAM file
|
||||
pattern: "*.sorted.bam"
|
||||
- pileup:
|
||||
type: file
|
||||
description: SAMtools pileup file
|
||||
pattern: "*.pileup"
|
||||
|
||||
authors:
|
||||
- "@jvhagey"
|
||||
@ -0,0 +1,49 @@
|
||||
def VERSION = '1.8.3'
|
||||
|
||||
process VARDICTJAVA {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0':
|
||||
'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai), path(bed)
|
||||
tuple path(fasta), path(fasta_fai)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.vcf.gz"), emit: vcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def args2 = task.ext.args2 ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
||||
"""
|
||||
vardict-java \\
|
||||
$args \\
|
||||
-c 1 -S 2 -E 3 \\
|
||||
-b $bam \\
|
||||
-th $task.cpus \\
|
||||
-N $prefix \\
|
||||
-G $fasta \\
|
||||
$bed \\
|
||||
| teststrandbias.R \\
|
||||
| var2vcf_valid.pl \\
|
||||
$args2 \\
|
||||
-N $prefix \\
|
||||
| gzip -c > ${prefix}.vcf.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
vardict-java: $VERSION
|
||||
var2vcf_valid.pl: \$(echo \$(var2vcf_valid.pl -h | sed -n 2p | awk '{ print \$2 }'))
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,60 @@
|
||||
name: "vardictjava"
|
||||
|
||||
description: The Java port of the VarDict variant caller
|
||||
keywords:
|
||||
- variant calling
|
||||
- VarDict
|
||||
- AstraZeneca
|
||||
tools:
|
||||
- "vardictjava":
|
||||
description: "Java port of the VarDict variant discovery program"
|
||||
homepage: "https://github.com/AstraZeneca-NGS/VarDictJava"
|
||||
documentation: "https://github.com/AstraZeneca-NGS/VarDictJava"
|
||||
tool_dev_url: "https://github.com/AstraZeneca-NGS/VarDictJava"
|
||||
doi: "10.1093/nar/gkw227 "
|
||||
licence: "['MIT']"
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM/SAM file
|
||||
pattern: "*.{bam,sam}"
|
||||
- bai:
|
||||
type: file
|
||||
description: Index of the BAM file
|
||||
pattern: "*.bai"
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA of the reference genome
|
||||
pattern: "*.{fa,fasta}"
|
||||
- fasta_fai:
|
||||
type: file
|
||||
description: The index of the FASTA of the reference genome
|
||||
pattern: "*.fai"
|
||||
- bed:
|
||||
type: file
|
||||
description: BED with the regions of interest
|
||||
pattern: "*.bed"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF file output
|
||||
pattern: "*.vcf.gz"
|
||||
|
||||
authors:
|
||||
- "@nvnieuwk"
|
||||
@ -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
|
||||
}
|
||||
@ -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"
|
||||
@ -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
|
||||
}
|
||||
@ -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
|
||||
}
|
||||
@ -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"
|
||||
@ -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
|
||||
}
|
||||
@ -0,0 +1,41 @@
|
||||
//
|
||||
// Run QC steps on BAM/CRAM files using Picard
|
||||
//
|
||||
|
||||
include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/picard/collectmultiplemetrics/main'
|
||||
include { PICARD_COLLECTWGSMETRICS } from '../../../modules/picard/collectwgsmetrics/main'
|
||||
include { PICARD_COLLECTHSMETRICS } from '../../../modules/picard/collecthsmetrics/main'
|
||||
|
||||
workflow BAM_QC_PICARD {
|
||||
take:
|
||||
ch_bam // channel: [ val(meta), [ bam ]]
|
||||
ch_fasta // channel: [ fasta ]
|
||||
ch_fasta_fai // channel: [ fasta_fai ]
|
||||
ch_bait_interval // channel: [ bait_interval ]
|
||||
ch_target_interval // channel: [ target_interval ]
|
||||
|
||||
main:
|
||||
ch_versions = Channel.empty()
|
||||
ch_coverage_metrics = Channel.empty()
|
||||
|
||||
PICARD_COLLECTMULTIPLEMETRICS( ch_bam, ch_fasta )
|
||||
ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
|
||||
|
||||
if (ch_bait_interval || ch_target_interval) {
|
||||
if (!ch_bait_interval) log.error("Bait interval channel is empty")
|
||||
if (!ch_target_interval) log.error("Target interval channel is empty")
|
||||
PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, ch_fasta_fai, ch_bait_interval, ch_target_interval )
|
||||
ch_coverage_metrics = ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.metrics)
|
||||
ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
|
||||
} else {
|
||||
PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )
|
||||
ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first())
|
||||
ch_coverage_metrics = ch_coverage_metrics.mix(PICARD_COLLECTWGSMETRICS.out.metrics)
|
||||
}
|
||||
|
||||
emit:
|
||||
coverage_metrics = ch_coverage_metrics // channel: [ val(meta), [ coverage_metrics ] ]
|
||||
multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), [ multiple_metrics ] ]
|
||||
|
||||
versions = ch_versions // channel: [ versions.yml ]
|
||||
}
|
||||
@ -0,0 +1,60 @@
|
||||
name: bam_qc
|
||||
description: Produces comprehensive statistics from BAM file
|
||||
keywords:
|
||||
- statistics
|
||||
- counts
|
||||
- hs_metrics
|
||||
- wgs_metrics
|
||||
- bam
|
||||
- sam
|
||||
- cram
|
||||
modules:
|
||||
- picard/collectmultiplemetrics
|
||||
- picard/collectwgsmetrics
|
||||
- picard/collecthsmetrics
|
||||
input:
|
||||
- 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}"
|
||||
- fasta:
|
||||
type: optional file
|
||||
description: Reference fasta file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- fasta_fai:
|
||||
type: optional file
|
||||
description: Reference fasta file index
|
||||
pattern: "*.{fasta,fa}.fai"
|
||||
- bait_intervals:
|
||||
type: optional file
|
||||
description: An interval list file that contains the locations of the baits used.
|
||||
pattern: "baits.interval_list"
|
||||
- target_intervals:
|
||||
type: optional file
|
||||
description: An interval list file that contains the locations of the targets.
|
||||
pattern: "targets.interval_list"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- coverage_metrics:
|
||||
type: file
|
||||
description: Alignment metrics files generated by picard CollectHsMetrics or CollectWgsMetrics
|
||||
pattern: "*_metrics.txt"
|
||||
- multiple_metrics:
|
||||
type: file
|
||||
description: Alignment metrics files generated by picard CollectMultipleMetrics
|
||||
pattern: "*_{metrics}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@matthdsm"
|
||||
@ -1,10 +1,23 @@
|
||||
- name: bamtools split test_bamtools_split
|
||||
command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
|
||||
- name: bamtools split test_bamtools_split_single_input
|
||||
command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_single_input -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
|
||||
tags:
|
||||
- bamtools/split
|
||||
- bamtools
|
||||
- bamtools/split
|
||||
files:
|
||||
- path: output/bamtools/test.paired_end.sorted.REF_chr22.bam
|
||||
- path: output/bamtools/test.REF_chr22.bam
|
||||
md5sum: b7dc50e0edf9c6bfc2e3b0e6d074dc07
|
||||
- path: output/bamtools/test.paired_end.sorted.REF_unmapped.bam
|
||||
- path: output/bamtools/test.REF_unmapped.bam
|
||||
md5sum: e0754bf72c51543b2d745d96537035fb
|
||||
- path: output/bamtools/versions.yml
|
||||
|
||||
- name: bamtools split test_bamtools_split_multiple
|
||||
command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_multiple -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
|
||||
tags:
|
||||
- bamtools
|
||||
- bamtools/split
|
||||
files:
|
||||
- path: output/bamtools/test.REF_chr22.bam
|
||||
md5sum: 585675bea34c48ebe9db06a561d4b4fa
|
||||
- path: output/bamtools/test.REF_unmapped.bam
|
||||
md5sum: 16ad644c87b9471f3026bc87c98b4963
|
||||
- path: output/bamtools/versions.yml
|
||||
|
||||
@ -1,5 +1,16 @@
|
||||
params {
|
||||
force_large_index = false
|
||||
}
|
||||
|
||||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
}
|
||||
|
||||
if (params.force_large_index) {
|
||||
process {
|
||||
withName: BOWTIE2_BUILD {
|
||||
ext.args = '--large-index'
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -1,8 +1,17 @@
|
||||
- name: diamond blastp
|
||||
command: nextflow run ./tests/modules/diamond/blastp -entry test_diamond_blastp -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastp/nextflow.config
|
||||
- name: diamond blastp test_diamond_blastp
|
||||
command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp -c tests/config/nextflow.config
|
||||
tags:
|
||||
- diamond/blastp
|
||||
- diamond
|
||||
files:
|
||||
- path: output/diamond/test.diamond_blastp.txt
|
||||
- path: output/diamond/versions.yml
|
||||
|
||||
- name: diamond blastp test_diamond_blastp_daa
|
||||
command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp_daa -c tests/config/nextflow.config
|
||||
tags:
|
||||
- diamond/blastp
|
||||
- diamond
|
||||
files:
|
||||
- path: ./output/diamond/test.diamond_blastp.txt
|
||||
md5sum: 3ca7f6290c1d8741c573370e6f8b4db0
|
||||
- path: output/diamond/test.diamond_blastp.daa
|
||||
- path: output/diamond/versions.yml
|
||||
|
||||
@ -1,8 +1,18 @@
|
||||
- name: diamond blastx
|
||||
command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastx/nextflow.config
|
||||
- name: diamond blastx test_diamond_blastx
|
||||
command: nextflow run tests/modules/diamond/blastx -entry test_diamond_blastx -c tests/config/nextflow.config
|
||||
tags:
|
||||
- diamond
|
||||
- diamond/blastx
|
||||
files:
|
||||
- path: ./output/diamond/test.diamond_blastx.txt
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
- path: output/diamond/test.diamond_blastx.txt
|
||||
- path: output/diamond/versions.yml
|
||||
|
||||
- name: diamond blastx test_diamond_blastx_daa
|
||||
command: nextflow run tests/modules/diamond/blastx -entry test_diamond_blastx_daa -c tests/config/nextflow.config
|
||||
tags:
|
||||
- diamond
|
||||
- diamond/blastx
|
||||
files:
|
||||
- path: output/diamond/test.diamond_blastx.daa
|
||||
md5sum: 0df4a833408416f32981415873facc11
|
||||
- path: output/diamond/versions.yml
|
||||
|
||||
@ -1,8 +1,9 @@
|
||||
- name: diamond makedb test_diamond_makedb
|
||||
command: nextflow run ./tests/modules/diamond/makedb -entry test_diamond_makedb -c ./tests/config/nextflow.config -c ./tests/modules/diamond/makedb/nextflow.config
|
||||
command: nextflow run tests/modules/diamond/makedb -entry test_diamond_makedb -c tests/config/nextflow.config
|
||||
tags:
|
||||
- diamond
|
||||
- diamond/makedb
|
||||
- diamond
|
||||
files:
|
||||
- path: output/diamond/genome.fasta.dmnd
|
||||
md5sum: 2447fb376394c20d43ea3aad2aa5d15d
|
||||
- path: output/diamond/proteome.fasta.dmnd
|
||||
md5sum: fc28c50b202dd7a7c5451cddff2ba1f4
|
||||
- path: output/diamond/versions.yml
|
||||
|
||||
@ -0,0 +1,17 @@
|
||||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { ELPREP_SPLIT } from '../../../../modules/elprep/split/main.nf'
|
||||
include { ELPREP_MERGE } from '../../../../modules/elprep/merge/main.nf'
|
||||
|
||||
workflow test_elprep_merge {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
|
||||
]
|
||||
|
||||
ELPREP_SPLIT ( input )
|
||||
ELPREP_MERGE ( ELPREP_SPLIT.out.bam )
|
||||
}
|
||||
@ -0,0 +1,5 @@
|
||||
process {
|
||||
withName : ELPREP_MERGE {
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,8 @@
|
||||
- name: elprep merge test_elprep_merge
|
||||
command: nextflow run tests/modules/elprep/merge -entry test_elprep_merge -c tests/config/nextflow.config
|
||||
tags:
|
||||
- elprep
|
||||
- elprep/merge
|
||||
files:
|
||||
- path: output/elprep/output/test.bam
|
||||
- path: output/elprep/versions.yml
|
||||
Some files were not shown because too many files have changed in this diff Show More
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Reference in New Issue