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64
.github/ISSUE_TEMPLATE/bug_report.md vendored
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---
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. -->

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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] -->

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---
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. -->

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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.

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.github/ISSUE_TEMPLATE/new_module.md vendored
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---
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

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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

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modules/allelecounter/meta.yml
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@ -32,8 +32,8 @@ input:
description: loci file <CHR><tab><POS1> description: loci file <CHR><tab><POS1>
pattern: "*.{tsv}" pattern: "*.{tsv}"
- fasta: - fasta:
type: file type: file
description: Input genome fasta file. Required when passing CRAM files. description: Input genome fasta file. Required when passing CRAM files.
output: output:
- meta: - meta:

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modules/amplify/predict/main.nf Normal file
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def VERSION = '1.0.3' // Version information not provided by tool
process AMPLIFY_PREDICT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::amplify=1.0.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/amplify:1.0.3--py36hdfd78af_0':
'quay.io/biocontainers/amplify:1.0.3--py36hdfd78af_0' }"
input:
tuple val(meta), path(faa)
path(model_dir)
output:
tuple val(meta), path('*.tsv'), emit: tsv
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def custom_model_dir = model_dir ? "-md ${model_dir}" : ""
"""
AMPlify \\
$args \\
${custom_model_dir} \\
-s '${faa}'
#rename output, because tool includes date and time in name
mv *.tsv ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
AMPlify: $VERSION
END_VERSIONS
"""
}

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modules/amplify/predict/meta.yml Normal file
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name: "amplify_predict"
description: AMPlify is an attentive deep learning model for antimicrobial peptide prediction.
keywords:
- antimicrobial peptides
- AMPs
- prediction
- model
tools:
- "amplify":
description: "Attentive deep learning model for antimicrobial peptide prediction"
homepage: "https://github.com/bcgsc/AMPlify"
documentation: "https://github.com/bcgsc/AMPlify"
tool_dev_url: "https://github.com/bcgsc/AMPlify"
doi: "https://doi.org/10.1186/s12864-022-08310-4"
licence: "['GPL v3']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- faa:
type: file
description: amino acid sequences fasta
pattern: "*.{fa,fa.gz,faa,faa.gz,fasta,fasta.gz}"
- model_dir:
type: directory
description: Directory of where models are stored (optional)
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- tsv:
type: file
description: amino acid sequences with prediction (AMP, non-AMP) and probability scores
pattern: "*.{tsv}"
authors:
- "@louperelo"

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modules/antismash/antismashlitedownloaddatabases/main.nf Normal file
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process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
label 'process_low'
conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
/*
These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH.
Reason: Upon execution, the tool checks if certain database files are present within the container and if not, it tries to create them in /usr/local/bin, for which only root user has write permissions. Mounting those database files with this module prevents the tool from trying to create them.
These files are also emitted as output channels in this module to enable the antismash-lite module to use them as mount volumes to the docker/singularity containers.
*/
containerOptions {
workflow.containerEngine == 'singularity' ?
"-B $database_css:/usr/local/lib/python3.8/site-packages/antismash/outputs/html/css,$database_detection:/usr/local/lib/python3.8/site-packages/antismash/detection,$database_modules:/usr/local/lib/python3.8/site-packages/antismash/modules" :
workflow.containerEngine == 'docker' ?
"-v \$PWD/$database_css:/usr/local/lib/python3.8/site-packages/antismash/outputs/html/css -v \$PWD/$database_detection:/usr/local/lib/python3.8/site-packages/antismash/detection -v \$PWD/$database_modules:/usr/local/lib/python3.8/site-packages/antismash/modules" :
''
}
input:
path database_css
path database_detection
path database_modules
output:
path("antismash_db") , emit: database
path("antismash_dir"), emit: antismash_dir
path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
conda = params.enable_conda
"""
download-antismash-databases \\
--database-dir antismash_db \\
$args
if [[ $conda = false ]]; \
then \
cp -r /usr/local/lib/python3.8/site-packages/antismash antismash_dir; \
else \
cp -r \$(python -c 'import antismash;print(antismash.__file__.split("/__")[0])') antismash_dir; \
fi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
END_VERSIONS
"""
}

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modules/antismash/antismashlitedownloaddatabases/meta.yml Normal file
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name: antismash_antismashlitedownloaddatabases
description: antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases.
keywords:
- secondary metabolites
- BGC
- biosynthetic gene cluster
- genome mining
- NRPS
- RiPP
- antibiotics
- prokaryotes
- bacteria
- eukaryotes
- fungi
- antismash
- database
tools:
- antismash:
description: antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell
homepage: https://docs.antismash.secondarymetabolites.org
documentation: https://docs.antismash.secondarymetabolites.org
tool_dev_url: https://github.com/antismash/antismash
doi: "10.1093/nar/gkab335"
licence: ["AGPL v3"]
input:
- database_css:
type: directory
description: |
antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
pattern: "css"
- database_detection:
type: directory
description: |
antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
pattern: "detection"
- database_modules:
type: directory
description: |
antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
pattern: "modules"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- database:
type: directory
description: Download directory for antiSMASH databases
pattern: "antismash_db"
- antismash_dir:
type: directory
description: |
antismash installation folder which is being modified during the antiSMASH database downloading step. The modified files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database and installation folder in pipelines.
pattern: "antismash_dir"
authors:
- "@jasmezz"

16
modules/bamtools/split/main.nf
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@ -2,10 +2,10 @@ process BAMTOOLS_SPLIT {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null) conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' : 'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0' :
'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }" 'quay.io/biocontainers/bamtools:2.5.2--hd03093a_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)
@ -20,11 +20,15 @@ process BAMTOOLS_SPLIT {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def input_list = bam.collect{"-in $it"}.join(' ')
""" """
bamtools \\ bamtools \\
split \\ merge \\
-in $bam \\ $input_list \\
$args | bamtools \\
split \\
-stub $prefix \\
$args
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

3
modules/bamtools/split/meta.yml
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@ -23,7 +23,7 @@ input:
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- bam: - bam:
type: file type: file
description: A BAM file to split description: A list of one or more BAM files to merge and then split
pattern: "*.bam" pattern: "*.bam"
output: output:
@ -43,3 +43,4 @@ output:
authors: authors:
- "@sguizard" - "@sguizard"
- "@matthdsm"

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modules/bclconvert/.gitignore vendored Normal file
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bcl-convert
*.rpm

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modules/bclconvert/Dockerfile Normal file
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# Dockerfile to create container with bcl-convert
# Push to nfcore/bclconvert:<VER>
FROM debian:bullseye-slim
LABEL authors="Matthias De Smet <matthias.desmet@ugent.be>" \
description="Docker image containing bcl-convert"
# Disclaimer: this container is not provided nor supported by Illumina
# 'ps' command is need by some nextflow executions to collect system stats
# Install procps and clean apt cache
RUN apt-get update \
&& apt-get install -y \
procps \
&& apt-get clean -y && rm -rf /var/lib/apt/lists/*
COPY bcl-convert /usr/local/bin/bcl-convert
RUN chmod +x /usr/local/bin/bcl-convert

30
modules/bclconvert/LICENSE Normal file
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@ -0,0 +1,30 @@
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17
modules/bclconvert/README.md Normal file
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@ -0,0 +1,17 @@
# Updating the docker container and making a new module release
bcl-convert is a commercial tool from Illumina. The container provided for the bcl-convert nf-core module is not provided nor supported by Illumina. Updating the bcl-convert versions in the container and pushing the update to Dockerhub needs to be done manually.
1. Navigate to the appropriate download page. - [BCL Convert](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/downloads.html): download the rpm of the desired bcl-convert version with `curl` or `wget`.
2. Unpack the RPM package using `rpm2cpio bcl-convert-*.rpm | cpio -i --make-directories`. Place the executable located in `<unpack_dir>/usr/bin/bcl-convert` in the same folder where the Dockerfile lies.
3. Create and test the container:
```bash
docker build . -t nfcore/bclconvert:<VERSION>
```
4. Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.
```bash
docker push nfcore/bclconvert:<VERSION>
```

81
modules/bclconvert/main.nf Normal file
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@ -0,0 +1,81 @@
process BCLCONVERT {
tag '$samplesheet'
label 'process_high'
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using bcl-convert. Please use docker or singularity containers."
}
container "nfcore/bclconvert:3.9.3"
input:
path samplesheet
path run_dir
output:
path "*.fastq.gz" ,emit: fastq
path "Reports/*.{csv,xml,bin}" ,emit: reports
path "Logs/*.{log,txt}" ,emit: logs
path "InterOp/*.bin" ,emit: interop
path "versions.yml" ,emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
bcl-convert \
$args \\
--output-directory . \\
--bcl-input-directory ${run_dir} \\
--sample-sheet ${samplesheet} \\
--bcl-num-parallel-tiles ${task.cpus}
mkdir InterOp
cp ${run_dir}/InterOp/*.bin InterOp/
mv Reports/*.bin InterOp/
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
END_VERSIONS
"""
stub:
"""
echo "sample1_S1_L001_R1_001" > sample1_S1_L001_R1_001.fastq.gz
echo "sample1_S1_L001_R2_001" > sample1_S1_L001_R2_001.fastq.gz
echo "sample1_S1_L002_R1_001" > sample1_S1_L002_R1_001.fastq.gz
echo "sample1_S1_L002_R2_001" > sample1_S1_L002_R2_001.fastq.gz
echo "sample2_S2_L001_R1_001" > sample2_S2_L001_R1_001.fastq.gz
echo "sample2_S2_L001_R2_001" > sample2_S2_L001_R2_001.fastq.gz
echo "sample2_S2_L002_R1_001" > sample2_S2_L002_R1_001.fastq.gz
echo "sample2_S2_L002_R2_001" > sample2_S2_L002_R2_001.fastq.gz
mkdir Reports
echo "Adapter_Metrics" > Reports/Adapter_Metrics.csv
echo "Demultiplex_Stats" > Reports/Demultiplex_Stats.csv
echo "fastq_list" > Reports/fastq_list.csv
echo "Index_Hopping_Counts" > Reports/Index_Hopping_Counts.csv
echo "IndexMetricsOut" > Reports/IndexMetricsOut.bin
echo "Quality_Metrics" > Reports/Quality_Metrics.csv
echo "RunInfo" > Reports/RunInfo.xml
echo "SampleSheet" > Reports/SampleSheet.csv
echo "Top_Unknown_Barcodes" > Reports/Top_Unknown_Barcodes.csv
mkdir Logs
echo "Errors" > Logs/Errors.log
echo "FastqComplete" > Logs/FastqComplete.txt
echo "Info" > Logs/Info.log
echo "Warnings" > Logs/Warnings.log
mkdir InterOp/
echo "InterOp" > InterOp/InterOp.bin
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
END_VERSIONS
"""
}

45
modules/bclconvert/meta.yml Normal file
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@ -0,0 +1,45 @@
name: "bclconvert"
description: Demultiplex Illumina BCL files
keywords:
- demultiplex
- illumina
- fastq
tools:
- "bclconvert":
description: "Demultiplex Illumina BCL files"
homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html"
documentation: "https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/FrontPages/BCL_Convert.htm"
licence: "ILLUMINA"
input:
- samplesheet:
type: file
description: "Input samplesheet"
pattern: "*.{csv}"
- run_dir:
type: directory
description: "Input run directory containing RunInfo.xml and BCL data"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- fastq:
type: file
description: Demultiplexed FASTQ files
pattern: "*.{fastq.gz}"
- reports:
type: file
description: Demultiplexing Reports
pattern: "Reports/*.{csv,xml}"
- logs:
type: file
description: Log files
pattern: "Logs/*.{log,txt}"
- interop:
type: file
description: Interop files
pattern: "Interop/*.{bin}"
authors:
- "@matthdsm"

4
modules/bowtie2/align/main.nf
View file

@ -29,6 +29,8 @@ process BOWTIE2_ALIGN {
def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
""" """
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'` INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
[ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
bowtie2 \\ bowtie2 \\
-x \$INDEX \\ -x \$INDEX \\
-U $reads \\ -U $reads \\
@ -49,6 +51,8 @@ process BOWTIE2_ALIGN {
def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
""" """
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'` INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
[ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
bowtie2 \\ bowtie2 \\
-x \$INDEX \\ -x \$INDEX \\
-1 ${reads[0]} \\ -1 ${reads[0]} \\

84
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@ -0,0 +1,84 @@
process BUSCO {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::busco=5.3.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/busco:5.3.2--pyhdfd78af_0':
'quay.io/biocontainers/busco:5.3.2--pyhdfd78af_0' }"
input:
tuple val(meta), path('tmp_input/*')
each lineage // Required: lineage to check against, "auto" enables --auto-lineage instead
path busco_lineages_path // Recommended: path to busco lineages - downloads if not set
path config_file // Optional: busco configuration file
output:
tuple val(meta), path("*-busco.batch_summary.txt"), emit: batch_summary
tuple val(meta), path("short_summary.*.txt") , emit: short_summaries_txt, optional: true
tuple val(meta), path("short_summary.*.json") , emit: short_summaries_json, optional: true
tuple val(meta), path("*-busco") , emit: busco_dir
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}-${lineage}"
def busco_config = config_file ? "--config $config_file" : ''
def busco_lineage = lineage.equals('auto') ? '--auto-lineage' : "--lineage_dataset ${lineage}"
def busco_lineage_dir = busco_lineages_path ? "--offline --download_path ${busco_lineages_path}" : ''
"""
# Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
# Check for container variable initialisation script and source it.
if [ -f "/usr/local/env-activate.sh" ]; then
set +u # Otherwise, errors out because of various unbound variables
. "/usr/local/env-activate.sh"
set -u
fi
# If the augustus config directory is not writable, then copy to writeable area
if [ ! -w "\${AUGUSTUS_CONFIG_PATH}" ]; then
# Create writable tmp directory for augustus
AUG_CONF_DIR=\$( mktemp -d -p \$PWD )
cp -r \$AUGUSTUS_CONFIG_PATH/* \$AUG_CONF_DIR
export AUGUSTUS_CONFIG_PATH=\$AUG_CONF_DIR
echo "New AUGUSTUS_CONFIG_PATH=\${AUGUSTUS_CONFIG_PATH}"
fi
# Ensure the input is uncompressed
INPUT_SEQS=input_seqs
mkdir "\$INPUT_SEQS"
cd "\$INPUT_SEQS"
for FASTA in ../tmp_input/*; do
if [ "\${FASTA##*.}" == 'gz' ]; then
gzip -cdf "\$FASTA" > \$( basename "\$FASTA" .gz )
else
ln -s "\$FASTA" .
fi
done
cd ..
busco \\
--cpu $task.cpus \\
--in "\$INPUT_SEQS" \\
--out ${prefix}-busco \\
$busco_lineage \\
$busco_lineage_dir \\
$busco_config \\
$args
# clean up
rm -rf "\$INPUT_SEQS"
# Move files to avoid staging/publishing issues
mv ${prefix}-busco/batch_summary.txt ${prefix}-busco.batch_summary.txt
mv ${prefix}-busco/*/short_summary.*.{json,txt} . || echo "Short summaries were not available: No genes were found."
cat <<-END_VERSIONS > versions.yml
"${task.process}":
busco: \$( busco --version 2>&1 | sed 's/^BUSCO //' )
END_VERSIONS
"""
}

69
modules/busco/meta.yml Normal file
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@ -0,0 +1,69 @@
name: busco
description: Benchmarking Universal Single Copy Orthologs
keywords:
- quality control
- genome
- transcriptome
- proteome
tools:
- busco:
description: BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
homepage: https://busco.ezlab.org/
documentation: https://busco.ezlab.org/busco_userguide.html
tool_dev_url: https://gitlab.com/ezlab/busco
doi: "10.1007/978-1-4939-9173-0_14"
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: Nucleic or amino acid sequence file in FASTA format.
pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}"
- lineage:
type: value
description: The BUSCO lineage to use, or "auto" to automatically select lineage
- busco_lineages_path:
type: directory
description: Path to local BUSCO lineages directory.
- config_file:
type: file
description: Path to BUSCO config file.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- batch_summary:
type: file
description: Summary of all sequence files analyzed
pattern: "*-busco.batch_summary.txt"
- short_summaries_txt:
type: file
description: Short Busco summary in plain text format
pattern: "short_summary.*.txt"
- short_summaries_json:
type: file
description: Short Busco summary in JSON format
pattern: "short_summary.*.json"
- busco_dir:
type: directory
description: BUSCO lineage specific output
pattern: "*-busco"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@priyanka-surana"
- "@charles-plessy"
- "@mahesh-panchal"
- "@muffato"
- "@jvhagey"

4
modules/cat/fastq/main.nf
View file

@ -4,8 +4,8 @@ process CAT_FASTQ {
conda (params.enable_conda ? "conda-forge::sed=4.7" : null) conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'biocontainers/biocontainers:v1.2.0_cv1' }" 'ubuntu:20.04' }"
input: input:
tuple val(meta), path(reads, stageAs: "input*/*") tuple val(meta), path(reads, stageAs: "input*/*")

23
modules/cnvpytor/callcnvs/main.nf
View file

@ -2,43 +2,42 @@ process CNVPYTOR_CALLCNVS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null) conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2': 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0':
'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }" 'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
input: input:
tuple val(meta), path(pytor) tuple val(meta), path(pytor)
val bin_sizes
output: output:
tuple val(meta), path("*.tsv"), emit: cnvs tuple val(meta), path("${pytor.baseName}.pytor") , emit: pytor
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
script: script:
def args = task.ext.args ?: '1000' def bins = bin_sizes ?: '1000'
def prefix = task.ext.prefix ?: "${meta.id}"
""" """
cnvpytor \\ cnvpytor \\
-root $pytor \\ -root $pytor \\
-call $args > ${prefix}.tsv -call $bin_sizes
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' )) cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
END_VERSIONS END_VERSIONS
""" """
stub: stub:
def prefix = task.ext.prefix ?: "${meta.id}"
""" """
touch ${prefix}.tsv touch ${pytor.baseName}.pytor
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' )) cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
END_VERSIONS END_VERSIONS
""" """
} }

11
modules/cnvpytor/callcnvs/meta.yml
View file

@ -17,8 +17,11 @@ input:
e.g. [ id:'test'] e.g. [ id:'test']
- pytor: - pytor:
type: file type: file
description: cnvpytor root file description: pytor file containing partitions of read depth histograms using mean-shift method
pattern: "*.{pytor}" pattern: "*.{pytor}"
- bin_sizes:
type: string
description: list of binsizes separated by space e.g. "1000 10000" and "1000"
output: output:
- meta: - meta:
@ -26,10 +29,10 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test' ] e.g. [ id:'test' ]
- cnvs: - pytor:
type: file type: file
description: file containing identified copy numer variations description: pytor files containing cnv calls
pattern: "*.{tsv}" pattern: "*.{pytor}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions

16
modules/cnvpytor/histogram/main.nf
View file

@ -2,13 +2,15 @@ process CNVPYTOR_HISTOGRAM {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null) conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2': 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0':
'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }" 'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
input: input:
tuple val(meta), path(pytor) tuple val(meta), path(pytor)
val bin_sizes
output: output:
tuple val(meta), path("${pytor.baseName}.pytor") , emit: pytor tuple val(meta), path("${pytor.baseName}.pytor") , emit: pytor
@ -18,15 +20,15 @@ process CNVPYTOR_HISTOGRAM {
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
script: script:
def args = task.ext.args ?: '1000' def bins = bin_sizes ?: '1000'
""" """
cnvpytor \\ cnvpytor \\
-root $pytor \\ -root $pytor \\
-his $args -his $bins
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' )) cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
END_VERSIONS END_VERSIONS
""" """
@ -36,7 +38,7 @@ process CNVPYTOR_HISTOGRAM {
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' )) cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
END_VERSIONS END_VERSIONS
""" """
} }

4
modules/cnvpytor/histogram/meta.yml
View file

@ -22,6 +22,9 @@ input:
type: file type: file
description: pytor file containing read depth data description: pytor file containing read depth data
pattern: "*.{pytor}" pattern: "*.{pytor}"
- bin_sizes:
type: string
description: list of binsizes separated by space e.g. "1000 10000" and "1000"
output: output:
- meta: - meta:
@ -40,3 +43,4 @@ output:
authors: authors:
- "@sima-r" - "@sima-r"
- "@ramprasadn"

10
modules/cnvpytor/importreaddepth/main.nf
View file

@ -2,10 +2,10 @@ process CNVPYTOR_IMPORTREADDEPTH {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null) conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2': 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0':
'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }" 'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
input: input:
tuple val(meta), path(input_file), path(index) tuple val(meta), path(input_file), path(index)
@ -32,7 +32,7 @@ process CNVPYTOR_IMPORTREADDEPTH {
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' )) cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
END_VERSIONS END_VERSIONS
""" """
@ -43,7 +43,7 @@ process CNVPYTOR_IMPORTREADDEPTH {
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' )) cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
END_VERSIONS END_VERSIONS
""" """
} }

1
modules/cnvpytor/importreaddepth/meta.yml
View file

@ -52,3 +52,4 @@ output:
authors: authors:
- "@sima-r" - "@sima-r"
- "@ramprasadn"

15
modules/cnvpytor/partition/main.nf
View file

@ -2,13 +2,14 @@ process CNVPYTOR_PARTITION {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null) conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2': 'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0':
'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }" 'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
input: input:
tuple val(meta), path(pytor) tuple val(meta), path(pytor)
val bin_sizes
output: output:
tuple val(meta), path("${pytor.baseName}.pytor"), emit: pytor tuple val(meta), path("${pytor.baseName}.pytor"), emit: pytor
@ -18,15 +19,15 @@ process CNVPYTOR_PARTITION {
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
script: script:
def args = task.ext.args ?: '' def bins = bin_sizes ?: '1000'
""" """
cnvpytor \\ cnvpytor \\
-root $pytor \\ -root $pytor \\
-partition $args -partition $bins
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' )) cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
END_VERSIONS END_VERSIONS
""" """
@ -36,7 +37,7 @@ process CNVPYTOR_PARTITION {
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' )) cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
END_VERSIONS END_VERSIONS
""" """
} }

4
modules/cnvpytor/partition/meta.yml
View file

@ -22,6 +22,9 @@ input:
type: file type: file
description: pytor file containing read depth data description: pytor file containing read depth data
pattern: "*.{pytor}" pattern: "*.{pytor}"
- bin_sizes:
type: string
description: list of binsizes separated by space e.g. "1000 10000" and "1000"
output: output:
- meta: - meta:
@ -40,3 +43,4 @@ output:
authors: authors:
- "@sima-r" - "@sima-r"
- "@ramprasadn"

60
modules/cnvpytor/view/main.nf Normal file
View file

@ -0,0 +1,60 @@
process CNVPYTOR_VIEW {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0':
'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
input:
tuple val(meta), path(pytor_files)
val bin_sizes
val output_format
output:
tuple val(meta), path("*.vcf"), emit: vcf , optional: true
tuple val(meta), path("*.tsv"), emit: tsv , optional: true
tuple val(meta), path("*.xls"), emit: xls , optional: true
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def output_suffix = output_format ?: 'vcf'
def bins = bin_sizes ?: '1000'
def input = pytor_files.join(" ")
def prefix = task.ext.prefix ?: "${meta.id}"
"""
python3 <<CODE
import cnvpytor,os
binsizes = "${bins}".split(" ")
for binsize in binsizes:
file_list = "${input}".split(" ")
app = cnvpytor.Viewer(file_list, params={} )
outputfile = "{}_{}.{}".format("${prefix}",binsize.strip(),"${output_suffix}")
app.print_filename = outputfile
app.bin_size = int(binsize)
app.print_calls_file()
CODE
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
END_VERSIONS
"""
stub:
def output_suffix = output_format ?: 'vcf'
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.${output_suffix}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
END_VERSIONS
"""
}

56
modules/cnvpytor/view/meta.yml Normal file
View file

@ -0,0 +1,56 @@
name: cnvpytor_view
description: view function to generate vcfs
keywords:
- cnv calling
tools:
- cnvpytor:
description: calling CNVs using read depth
homepage: https://github.com/abyzovlab/CNVpytor
documentation: https://github.com/abyzovlab/CNVpytor
tool_dev_url: https://github.com/abyzovlab/CNVpytor
doi: "10.1101/2021.01.27.428472v1"
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- pytor_files:
type: file
description: pytor file containing cnv calls. To merge calls from multiple samples use a list of files.
pattern: "*.{pytor}"
- bin_sizes:
type: string
description: list of binsizes separated by space e.g. "1000 10000" and "1000"
- output_format:
type: string
description: output format of the cnv calls. Valid entries are "tsv", "vcf", and "xls"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- tsv:
type: file
description: tsv file containing cnv calls
pattern: "*.{tsv}"
- vcf:
type: file
description: vcf file containing cnv calls
pattern: "*.{vcf}"
- xls:
type: file
description: xls file containing cnv calls
pattern: "*.{xls}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@sima-r"
- "@ramprasadn"

6
modules/custom/getchromsizes/main.nf
View file

@ -2,10 +2,10 @@ process CUSTOM_GETCHROMSIZES {
tag "$fasta" tag "$fasta"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::samtools=1.15" : null) conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : 'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
'quay.io/biocontainers/samtools:1.15--h1170115_1' }" 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
input: input:
path fasta path fasta

40
modules/diamond/blastp/main.nf
View file

@ -2,20 +2,26 @@ process DIAMOND_BLASTP {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
// Dimaond is limited to v2.0.9 because there is not a conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
// singularity version higher than this at the current time.
conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' : 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }" 'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
input: input:
tuple val(meta), path(fasta) tuple val(meta), path(fasta)
path db path db
val out_ext
val blast_columns
output: output:
tuple val(meta), path('*.txt'), emit: txt tuple val(meta), path('*.blast'), optional: true, emit: blast
path "versions.yml" , emit: versions tuple val(meta), path('*.xml') , optional: true, emit: xml
tuple val(meta), path('*.txt') , optional: true, emit: txt
tuple val(meta), path('*.daa') , optional: true, emit: daa
tuple val(meta), path('*.sam') , optional: true, emit: sam
tuple val(meta), path('*.tsv') , optional: true, emit: tsv
tuple val(meta), path('*.paf') , optional: true, emit: paf
path "versions.yml" , emit: versions
when: when:
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
@ -23,6 +29,21 @@ process DIAMOND_BLASTP {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def columns = blast_columns ? "${blast_columns}" : ''
switch ( out_ext ) {
case "blast": outfmt = 0; break
case "xml": outfmt = 5; break
case "txt": outfmt = 6; break
case "daa": outfmt = 100; break
case "sam": outfmt = 101; break
case "tsv": outfmt = 102; break
case "paf": outfmt = 103; break
default:
outfmt = '6';
out_ext = 'txt';
log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
break
}
""" """
DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'` DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
@ -31,8 +52,9 @@ process DIAMOND_BLASTP {
--threads $task.cpus \\ --threads $task.cpus \\
--db \$DB \\ --db \$DB \\
--query $fasta \\ --query $fasta \\
--outfmt ${outfmt} ${columns} \\
$args \\ $args \\
--out ${prefix}.txt --out ${prefix}.${out_ext}
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

43
modules/diamond/blastp/meta.yml
View file

@ -28,12 +28,50 @@ input:
type: directory type: directory
description: Directory containing the protein blast database description: Directory containing the protein blast database
pattern: "*" pattern: "*"
- out_ext:
type: string
description: |
Specify the type of output file to be generated. `blast` corresponds to
BLAST pairwise format. `xml` corresponds to BLAST xml format.
`txt` corresponds to to BLAST tabular format. `tsv` corresponds to
taxonomic classification format.
pattern: "blast|xml|txt|daa|sam|tsv|paf"
- blast_columns:
type: string
description: |
Optional space separated list of DIAMOND tabular BLAST output keywords
used for in conjunction with the 'txt' out_ext option (--outfmt 6). See
DIAMOND documnetation for more information.
output: output:
- txt: - blast:
type: file type: file
description: File containing blastp hits description: File containing blastp hits
pattern: "*.{blastp.txt}" pattern: "*.{blast}"
- xml:
type: file
description: File containing blastp hits
pattern: "*.{xml}"
- txt:
type: file
description: File containing hits in tabular BLAST format.
pattern: "*.{txt}"
- daa:
type: file
description: File containing hits DAA format
pattern: "*.{daa}"
- sam:
type: file
description: File containing aligned reads in SAM format
pattern: "*.{sam}"
- tsv:
type: file
description: Tab separated file containing taxonomic classification of hits
pattern: "*.{tsv}"
- paf:
type: file
description: File containing aligned reads in pairwise mapping format format
pattern: "*.{paf}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
@ -41,3 +79,4 @@ output:
authors: authors:
- "@spficklin" - "@spficklin"
- "@jfy133"

40
modules/diamond/blastx/main.nf
View file

@ -2,20 +2,26 @@ process DIAMOND_BLASTX {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
// Dimaond is limited to v2.0.9 because there is not a conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
// singularity version higher than this at the current time.
conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' : 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }" 'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
input: input:
tuple val(meta), path(fasta) tuple val(meta), path(fasta)
path db path db
val out_ext
val blast_columns
output: output:
tuple val(meta), path('*.txt'), emit: txt tuple val(meta), path('*.blast'), optional: true, emit: blast
path "versions.yml" , emit: versions tuple val(meta), path('*.xml') , optional: true, emit: xml
tuple val(meta), path('*.txt') , optional: true, emit: txt
tuple val(meta), path('*.daa') , optional: true, emit: daa
tuple val(meta), path('*.sam') , optional: true, emit: sam
tuple val(meta), path('*.tsv') , optional: true, emit: tsv
tuple val(meta), path('*.paf') , optional: true, emit: paf
path "versions.yml" , emit: versions
when: when:
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
@ -23,6 +29,21 @@ process DIAMOND_BLASTX {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def columns = blast_columns ? "${blast_columns}" : ''
switch ( out_ext ) {
case "blast": outfmt = 0; break
case "xml": outfmt = 5; break
case "txt": outfmt = 6; break
case "daa": outfmt = 100; break
case "sam": outfmt = 101; break
case "tsv": outfmt = 102; break
case "paf": outfmt = 103; break
default:
outfmt = '6';
out_ext = 'txt';
log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
break
}
""" """
DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'` DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
@ -31,8 +52,9 @@ process DIAMOND_BLASTX {
--threads $task.cpus \\ --threads $task.cpus \\
--db \$DB \\ --db \$DB \\
--query $fasta \\ --query $fasta \\
--outfmt ${outfmt} ${columns} \\
$args \\ $args \\
--out ${prefix}.txt --out ${prefix}.${out_ext}
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

37
modules/diamond/blastx/meta.yml
View file

@ -28,12 +28,44 @@ input:
type: directory type: directory
description: Directory containing the nucelotide blast database description: Directory containing the nucelotide blast database
pattern: "*" pattern: "*"
- out_ext:
type: string
description: |
Specify the type of output file to be generated. `blast` corresponds to
BLAST pairwise format. `xml` corresponds to BLAST xml format.
`txt` corresponds to to BLAST tabular format. `tsv` corresponds to
taxonomic classification format.
pattern: "blast|xml|txt|daa|sam|tsv|paf"
output: output:
- blast:
type: file
description: File containing blastp hits
pattern: "*.{blast}"
- xml:
type: file
description: File containing blastp hits
pattern: "*.{xml}"
- txt: - txt:
type: file type: file
description: File containing blastx hits description: File containing hits in tabular BLAST format.
pattern: "*.{blastx.txt}" pattern: "*.{txt}"
- daa:
type: file
description: File containing hits DAA format
pattern: "*.{daa}"
- sam:
type: file
description: File containing aligned reads in SAM format
pattern: "*.{sam}"
- tsv:
type: file
description: Tab separated file containing taxonomic classification of hits
pattern: "*.{tsv}"
- paf:
type: file
description: File containing aligned reads in pairwise mapping format format
pattern: "*.{paf}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
@ -41,3 +73,4 @@ output:
authors: authors:
- "@spficklin" - "@spficklin"
- "@jfy133"

8
modules/diamond/makedb/main.nf
View file

@ -2,12 +2,10 @@ process DIAMOND_MAKEDB {
tag "$fasta" tag "$fasta"
label 'process_medium' label 'process_medium'
// Dimaond is limited to v2.0.9 because there is not a conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
// singularity version higher than this at the current time.
conda (params.enable_conda ? 'bioconda::diamond=2.0.9' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' : 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }" 'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
input: input:
path fasta path fasta

89
modules/elprep/filter/main.nf Normal file
View file

@ -0,0 +1,89 @@
process ELPREP_FILTER {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null)
container "${ 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' }"
input:
tuple val(meta), path(bam)
val(run_haplotypecaller)
val(run_bqsr)
path(reference_sequences)
path(filter_regions_bed)
path(reference_elfasta)
path(known_sites_elsites)
path(target_regions_bed)
path(intermediate_bqsr_tables)
val(bqsr_tables_only)
val(get_activity_profile)
val(get_assembly_regions)
output:
tuple val(meta), path("output/**.{bam,sam}") ,emit: bam
tuple val(meta), path("*.metrics.txt") ,optional: true, emit: metrics
tuple val(meta), path("*.recall") ,optional: true, emit: recall
tuple val(meta), path("*.vcf.gz") ,optional: true, emit: gvcf
tuple val(meta), path("*.table") ,optional: true, emit: table
tuple val(meta), path("*.activity_profile.igv") ,optional: true, emit: activity_profile
tuple val(meta), path("*.assembly_regions.igv") ,optional: true, emit: assembly_regions
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 suffix = args.contains("--output-type sam") ? "sam" : "bam"
// filter args
def reference_sequences_cmd = reference_sequences ? " --replace-reference-sequences ${reference_sequences}" : ""
def filter_regions_cmd = filter_regions_bed ? " --filter-non-overlapping-reads ${filter_regions_bed}" : ""
// markdup args
def markdup_cmd = args.contains("--mark-duplicates") ? " --mark-optical-duplicates ${prefix}.metrics.txt": ""
// variant calling args
def haplotyper_cmd = run_haplotypecaller ? " --haplotypecaller ${prefix}.g.vcf.gz": ""
def fasta_cmd = reference_elfasta ? " --reference ${reference_elfasta}": ""
def known_sites_cmd = known_sites_elsites ? " --known-sites ${known_sites_elsites}": ""
def target_regions_cmd = target_regions_bed ? " --target-regions ${target_regions_bed}": ""
// bqsr args
def bqsr_cmd = run_bqsr ? " --bqsr ${prefix}.recall": ""
def bqsr_tables_only_cmd = bqsr_tables_only ? " --bqsr-tables-only ${prefix}.table": ""
def intermediate_bqsr_cmd = intermediate_bqsr_tables ? " --bqsr-apply .": ""
// misc
def activity_profile_cmd = get_activity_profile ? " --activity-profile ${prefix}.activity_profile.igv": ""
def assembly_regions_cmd = get_assembly_regions ? " --assembly-regions ${prefix}.assembly_regions.igv": ""
"""
elprep filter ${bam} output/${prefix}.${suffix} \\
${reference_sequences_cmd} \\
${filter_regions_cmd} \\
${markdup_cmd} \\
${haplotyper_cmd} \\
${fasta_cmd} \\
${known_sites_cmd} \\
${target_regions_cmd} \\
${bqsr_cmd} \\
${bqsr_tables_only_cmd} \\
${intermediate_bqsr_cmd} \\
${activity_profile_cmd} \\
${assembly_regions_cmd} \\
--nr-of-threads ${task.cpus} \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//')
END_VERSIONS
"""
}

106
modules/elprep/filter/meta.yml Normal file
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@ -0,0 +1,106 @@
name: "elprep_filter"
description: "Filter, sort and markdup sam/bam files, with optional BQSR and variant calling."
keywords:
- sort
- bam
- sam
- filter
- variant calling
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: Input SAM/BAM file
pattern: "*.{bam,sam}"
- run_haplotypecaller:
type: boolean
description: Run variant calling on the input files. Needed to generate gvcf output.
- run_bqsr:
type: boolean
description: Run BQSR on the input files. Needed to generate recall metrics.
- reference_sequences:
type: file
description: Optional SAM header to replace existing header.
pattern: "*.sam"
- filter_regions_bed:
type: file
description: Optional BED file containing regions to filter.
pattern: "*.bed"
- reference_elfasta:
type: file
description: Elfasta file, required for BQSR and variant calling.
pattern: "*.elfasta"
- known_sites:
type: file
description: Optional elsites file containing known SNPs for BQSR.
pattern: "*.elsites"
- target_regions_bed:
type: file
description: Optional BED file containing target regions for BQSR and variant calling.
pattern: "*.bed"
- intermediate_bqsr_tables:
type: file
description: Optional list of BQSR tables, used when parsing files created by `elprep split`
pattern: "*.table"
- bqsr_tables_only:
type: boolean
description: Write intermediate BQSR tables, used when parsing files created by `elprep split`.
- get_activity_profile:
type: boolean
description: Get the activity profile calculated by the haplotypecaller to the given file in IGV format.
- get_assembly_regions:
type: boolean
description: Get the assembly regions calculated by haplotypecaller to the speficied file in IGV format.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam:
type: file
description: Sorted, markdup, optionally BQSR BAM/SAM file
pattern: "*.{bam,sam}"
- metrics:
type: file
description: Optional duplicate metrics file generated by elprep
pattern: "*.{metrics.txt}"
- recall:
type: file
description: Optional recall metrics file generated by elprep
pattern: "*.{recall}"
- gvcf:
type: file
description: Optional GVCF output file
pattern: "*.{vcf.gz}"
- table:
type: file
description: Optional intermediate BQSR table output file
pattern: "*.{table}"
- activity_profile:
type: file
description: Optional activity profile output file
pattern: "*.{activity_profile.igv}"
- assembly_regions:
type: file
description: Optional activity regions output file
pattern: "*.{assembly_regions.igv}"
authors:
- "@matthdsm"

43
modules/elprep/merge/main.nf Normal file
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@ -0,0 +1,43 @@
process ELPREP_MERGE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null)
container "${ 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' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("output/**.{bam,sam}") , emit: bam
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def 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
mv ${bam} input/
elprep merge \\
input/ \\
output/${prefix}.${suffix} \\
$args \\
${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
"""
}

44
modules/elprep/merge/meta.yml Normal file
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@ -0,0 +1,44 @@
name: "elprep_merge"
description: Merge split bam/sam chunks in one file
keywords:
- bam
- 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
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
#
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam:
type: file
description: Merged BAM/SAM file
pattern: "*.{bam,sam}"
authors:
- "@matthdsm"

45
modules/elprep/split/main.nf Normal file
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@ -0,0 +1,45 @@
process ELPREP_SPLIT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null)
container "${ 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' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("output/**.{bam,sam}"), emit: bam
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def single_end = meta.single_end ? " --single-end": ""
"""
# create directory and move all input so elprep can find and merge them before splitting
mkdir input
mv ${bam} input/
mkdir ${prefix}
elprep split \\
input \\
output/ \\
$args \\
$single_end \\
--nr-of-threads $task.cpus \\
--output-prefix $prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//')
END_VERSIONS
"""
}

43
modules/elprep/split/meta.yml Normal file
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@ -0,0 +1,43 @@
name: "elprep_split"
description: Split bam file into manageable chunks
keywords:
- bam
- split by chromosome
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"
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 files
pattern: "*.{bam,sam}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
#
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam:
type: file
description: List of split BAM/SAM files
pattern: "*.{bam,sam}"
authors:
- "@matthdsm"

11
modules/ensemblvep/Dockerfile
View file

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

5
modules/ensemblvep/build.sh
View file

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

1
modules/ensemblvep/main.nf
View file

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

15
modules/ensemblvep/meta.yml
View file

@ -10,17 +10,6 @@ tools:
homepage: https://www.ensembl.org/info/docs/tools/vep/index.html homepage: https://www.ensembl.org/info/docs/tools/vep/index.html
documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html
licence: ["Apache-2.0"] 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: input:
- meta: - meta:
type: map type: map
@ -47,6 +36,10 @@ input:
type: file type: file
description: | description: |
path to VEP cache (optional) path to VEP cache (optional)
- extra_files:
type: tuple
description: |
path to file(s) needed for plugins (optional)
output: output:
- vcf: - vcf:
type: file type: file

41
modules/gamma/main.nf Normal file
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@ -0,0 +1,41 @@
def VERSION = '2.1' // Version information not provided by tool on CLI
process GAMMA {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gamma=2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gamma%3A2.1--hdfd78af_0':
'quay.io/biocontainers/gamma:2.1--hdfd78af_0' }"
input:
tuple val(meta), path(fasta)
path(db)
output:
tuple val(meta), path("*.gamma") , emit: gamma
tuple val(meta), path("*.psl") , emit: psl
tuple val(meta), path("*.gff") , optional:true , emit: gff
tuple val(meta), path("*.fasta"), optional:true , emit: fasta
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}"
"""
GAMMA.py \\
$args \\
$fasta \\
$db \\
$prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gamma: $VERSION
END_VERSIONS
"""
}

63
modules/gamma/meta.yml Normal file
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@ -0,0 +1,63 @@
name: "gamma"
description: Gene Allele Mutation Microbial Assessment
keywords:
- gamma
- gene-calling
tools:
- "gamma":
description: "Tool for Gene Allele Mutation Microbial Assessment"
homepage: "https://github.com/rastanton/GAMMA"
documentation: "https://github.com/rastanton/GAMMA"
tool_dev_url: "https://github.com/rastanton/GAMMA"
doi: "10.1093/bioinformatics/btab607"
licence: "['Apache License 2.0']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: FASTA file
pattern: "*.{fa,fasta}"
- db:
type: file
description: Database in FASTA format
pattern: "*.{fa,fasta}"
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"
- gamma:
type: file
description: GAMMA file with annotated gene matches
pattern: "*.{gamma}"
- psl:
type: file
description: PSL file with all gene matches found
pattern: "*.{psl}"
- gff:
type: file
description: GFF file
pattern: "*.{gff}"
- fasta:
type: file
description: multifasta file of the gene matches
pattern: "*.{fasta}"
authors:
- "@sateeshperi"
- "@rastanton"

2
modules/gatk4/haplotypecaller/main.nf
View file

@ -17,7 +17,7 @@ process GATK4_HAPLOTYPECALLER {
output: output:
tuple val(meta), path("*.vcf.gz"), emit: vcf tuple val(meta), path("*.vcf.gz"), emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi tuple val(meta), path("*.tbi") , optional:true, emit: tbi
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:

2
modules/gatk4/markduplicates/main.nf
View file

@ -12,7 +12,7 @@ process GATK4_MARKDUPLICATES {
output: output:
tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*.bam") , emit: bam
tuple val(meta), path("*.bai") , emit: bai tuple val(meta), path("*.bai") , optional:true, emit: bai
tuple val(meta), path("*.metrics"), emit: metrics tuple val(meta), path("*.metrics"), emit: metrics
path "versions.yml" , emit: versions path "versions.yml" , emit: versions

11
modules/gatk4/mergebamalignment/main.nf
View file

@ -43,4 +43,15 @@ process GATK4_MERGEBAMALIGNMENT {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
} }

14
modules/gatk4/mutect2/main.nf
View file

@ -57,4 +57,18 @@ process GATK4_MUTECT2 {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf.gz
touch ${prefix}.vcf.gz.tbi
touch ${prefix}.vcf.gz.stats
touch ${prefix}.f1r2.tar.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
} }

11
modules/gatk4/revertsam/main.nf
View file

@ -39,4 +39,15 @@ process GATK4_REVERTSAM {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.reverted.bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
} }

13
modules/gatk4/samtofastq/main.nf
View file

@ -40,4 +40,17 @@ process GATK4_SAMTOFASTQ {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.fastq.gz
touch ${prefix}_1.fastq.gz
touch ${prefix}_2.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
} }

4
modules/gatk4/splitncigarreads/main.nf
View file

@ -8,7 +8,7 @@ process GATK4_SPLITNCIGARREADS {
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam), path(bai), path(intervals)
path fasta path fasta
path fai path fai
path dict path dict
@ -23,6 +23,7 @@ process GATK4_SPLITNCIGARREADS {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def interval_command = intervals ? "--intervals $intervals" : ""
def avail_mem = 3 def avail_mem = 3
if (!task.memory) { if (!task.memory) {
@ -35,6 +36,7 @@ process GATK4_SPLITNCIGARREADS {
--input $bam \\ --input $bam \\
--output ${prefix}.bam \\ --output ${prefix}.bam \\
--reference $fasta \\ --reference $fasta \\
$interval_command \\
--tmp-dir . \\ --tmp-dir . \\
$args $args

7
modules/gatk4/splitncigarreads/meta.yml
View file

@ -23,6 +23,13 @@ input:
type: list type: list
description: BAM/SAM/CRAM file containing reads description: BAM/SAM/CRAM file containing reads
pattern: "*.{bam,sam,cram}" pattern: "*.{bam,sam,cram}"
- bai:
type: list
description: BAI/SAI/CRAI index file (optional)
pattern: "*.{bai,sai,crai}"
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- fasta: - fasta:
type: file type: file
description: The reference fasta file description: The reference fasta file

4
modules/gunzip/main.nf
View file

@ -4,8 +4,8 @@ process GUNZIP {
conda (params.enable_conda ? "conda-forge::sed=4.7" : null) conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'biocontainers/biocontainers:v1.2.0_cv1' }" 'ubuntu:20.04' }"
input: input:
tuple val(meta), path(archive) tuple val(meta), path(archive)

42
modules/happy/happy/main.nf Normal file
View file

@ -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
"""
}

67
modules/happy/happy/meta.yml Normal file
View file

@ -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"

41
modules/happy/prepy/main.nf Normal file
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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
"""
}

55
modules/happy/prepy/meta.yml Normal file
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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"

40
modules/kaiju/kaiju2table/main.nf Normal file
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@ -0,0 +1,40 @@
process KAIJU_KAIJU2TABLE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
'quay.io/biocontainers/kaiju:1.8.2--h2e03b76_0' }"
input:
tuple val(meta), path(results)
path db
val taxon_rank
output:
tuple val(meta), path('*.txt'), emit: summary
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}"
"""
dbnodes=`find -L ${db} -name "*nodes.dmp"`
dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
kaiju2table $args \\
-t \$dbnodes \\
-n \$dbname \\
-r ${taxon_rank} \\
-o ${prefix}.txt \\
${results}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
END_VERSIONS
"""
}

50
modules/kaiju/kaiju2table/meta.yml Normal file
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@ -0,0 +1,50 @@
name: "kaiju_kaiju2table"
description: write your description here
keywords:
- classify
- metagenomics
tools:
- kaiju:
description: Fast and sensitive taxonomic classification for metagenomics
homepage: https://kaiju.binf.ku.dk/
documentation: https://github.com/bioinformatics-centre/kaiju/blob/master/README.md
tool_dev_url: https://github.com/bioinformatics-centre/kaiju
doi: "10.1038/ncomms11257"
licence: ["GNU GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- results:
type: file
description: File containing the kaiju classification results
pattern: "*.{txt}"
- taxon_rank:
type: string
description: |
Taxonomic rank to display in report
pattern: "phylum|class|order|family|genus|species"
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"
- results:
type: file
description: |
Summary table for a given taxonomic rank
pattern: "*.{tsv}"
authors:
- "@sofstam"
- "@talnor"
- "@jfy133"

23
modules/kraken2/kraken2/main.nf
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@ -10,12 +10,15 @@ process KRAKEN2_KRAKEN2 {
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)
path db path db
val save_output_fastqs
val save_reads_assignment
output: output:
tuple val(meta), path('*classified*') , emit: classified tuple val(meta), path('*classified*') , optional:true, emit: classified_reads_fastq
tuple val(meta), path('*unclassified*'), emit: unclassified tuple val(meta), path('*unclassified*') , optional:true, emit: unclassified_reads_fastq
tuple val(meta), path('*report.txt') , emit: txt tuple val(meta), path('*classifiedreads*'), optional:true, emit: classified_reads_assignment
path "versions.yml" , emit: versions tuple val(meta), path('*report.txt') , emit: report
path "versions.yml" , emit: versions
when: when:
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
@ -26,19 +29,25 @@ process KRAKEN2_KRAKEN2 {
def paired = meta.single_end ? "" : "--paired" def paired = meta.single_end ? "" : "--paired"
def classified = meta.single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq" def classified = meta.single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq"
def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq" def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq"
def classified_command = save_output_fastqs ? "--classified-out ${classified}" : ""
def unclassified_command = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
def readclassification_command = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : ""
def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : ""
""" """
kraken2 \\ kraken2 \\
--db $db \\ --db $db \\
--threads $task.cpus \\ --threads $task.cpus \\
--unclassified-out $unclassified \\
--classified-out $classified \\
--report ${prefix}.kraken2.report.txt \\ --report ${prefix}.kraken2.report.txt \\
--gzip-compressed \\ --gzip-compressed \\
$unclassified_command \\
$classified_command \\
$readclassification_command \\
$paired \\ $paired \\
$args \\ $args \\
$reads $reads
pigz -p $task.cpus *.fastq $compress_reads_command
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

25
modules/kraken2/kraken2/meta.yml
View file

@ -27,25 +27,40 @@ input:
- db: - db:
type: directory type: directory
description: Kraken2 database description: Kraken2 database
- save_output_fastqs:
type: boolean
description: |
If true, optional commands are added to save classified and unclassified reads
as fastq files
- save_reads_assignment:
type: boolean
description: |
If true, an optional command is added to save a file reporting the taxonomic
classification of each input read
output: output:
- meta: - meta:
type: map type: map
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- classified: - classified_reads_fastq:
type: file type: file
description: | description: |
Reads classified to belong to any of the taxa Reads classified as belonging to any of the taxa
on the Kraken2 database. on the Kraken2 database.
pattern: "*{fastq.gz}" pattern: "*{fastq.gz}"
- unclassified: - unclassified_reads_fastq:
type: file type: file
description: | description: |
Reads not classified to belong to any of the taxa Reads not classified to any of the taxa
on the Kraken2 database. on the Kraken2 database.
pattern: "*{fastq.gz}" pattern: "*{fastq.gz}"
- txt: - classified_reads_assignment:
type: file
description: |
Kraken2 output file indicating the taxonomic assignment of
each input read
- report:
type: file type: file
description: | description: |
Kraken2 report containing stats about classified Kraken2 report containing stats about classified

4
modules/krona/kronadb/main.nf
View file

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

5
modules/krona/ktimporttaxonomy/main.nf
View file

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

7
modules/krona/ktimporttaxonomy/meta.yml
View file

@ -23,8 +23,11 @@ input:
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test'] e.g. [ id:'test']
- database: - database:
type: path type: file
description: "Path to the taxonomy database downloaded by krona/kronadb" 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: - report:
type: file 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." 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."

34
modules/krona/ktimporttext/main.nf Normal file
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@ -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
"""
}

47
modules/krona/ktimporttext/meta.yml Normal file
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@ -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"

30
modules/krona/ktupdatetaxonomy/main.nf Normal file
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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
"""
}

31
modules/krona/ktupdatetaxonomy/meta.yml Normal file
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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"

35
modules/md5sum/main.nf Normal file
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@ -0,0 +1,35 @@
process MD5SUM {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"
input:
tuple val(meta), path(file)
output:
tuple val(meta), path("*.md5"), emit: checksum
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}"
"""
md5sum \\
$args \\
${file} \\
> ${file}.md5
cat <<-END_VERSIONS > versions.yml
"${task.process}":
md5sum: \$(echo \$(md5sum --version 2>&1 | head -n 1| sed 's/^.*) //;' ))
END_VERSIONS
"""
}

39
modules/md5sum/meta.yml Normal file
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@ -0,0 +1,39 @@
name: "md5sum"
description: Create an MD5 (128-bit) checksum
keywords:
- checksum
tools:
- "md5sum":
description: Create an MD5 (128-bit) checksum
homepage: "https://www.gnu.org"
documentation: "https://man7.org/linux/man-pages/man1/md5sum.1.html"
licence: GPLv3+
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- file:
type: file
description: Any file
pattern: "*.*"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- checksum:
type: file
description: File containing checksum
pattern: "*.md5"
authors:
- "@matthdsm"

37
modules/meryl/count/main.nf Normal file
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@ -0,0 +1,37 @@
process MERYL_COUNT {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::meryl=1.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1':
'quay.io/biocontainers/meryl:1.3--h87f3376_1' }"
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*.meryldb"), emit: meryl_db
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}"
"""
for READ in $reads; do
meryl count \\
threads=$task.cpus \\
$args \\
$reads \\
output read.\${READ%.f*}.meryldb
done
cat <<-END_VERSIONS > versions.yml
"${task.process}":
meryl: \$( meryl --version |& sed 's/meryl //' )
END_VERSIONS
"""
}

43
modules/meryl/count/meta.yml Normal file
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@ -0,0 +1,43 @@
name: "meryl_count"
description: A genomic k-mer counter (and sequence utility) with nice features.
keywords:
- k-mer
- count
tools:
- "meryl":
description: "A genomic k-mer counter (and sequence utility) with nice features. "
homepage: "https://github.com/marbl/meryl"
documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html"
tool_dev_url: "https://github.com/marbl/meryl"
doi: ""
licence: "['GPL']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
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"
- meryl_db:
type: directory
description: A Meryl k-mer database
pattern: "*.meryldb"
authors:
- "@mahesh-panchal"

2
modules/metaphlan3/main.nf
View file

@ -23,7 +23,7 @@ process METAPHLAN3 {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def input_type = ("$input".endsWith(".fastq.gz")) ? "--input_type fastq" : ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam" def input_type = ("$input".endsWith(".fastq.gz") || "$input".endsWith(".fq.gz")) ? "--input_type fastq" : ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam"
def input_data = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input" def input_data = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input"
def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt" def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"

22
modules/minimap2/align/main.nf
View file

@ -2,18 +2,22 @@ process MINIMAP2_ALIGN {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null) conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' :
'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }" 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)
path reference path reference
val bam_format
val cigar_paf_format
val cigar_bam
output: output:
tuple val(meta), path("*.paf"), emit: paf tuple val(meta), path("*.paf"), optional: true, emit: paf
path "versions.yml" , emit: versions tuple val(meta), path("*.bam"), optional: true, emit: bam
path "versions.yml" , emit: versions
when: when:
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
@ -22,13 +26,19 @@ process MINIMAP2_ALIGN {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}" def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
""" """
minimap2 \\ minimap2 \\
$args \\ $args \\
-t $task.cpus \\ -t $task.cpus \\
$reference \\ $reference \\
$input_reads \\ $input_reads \\
> ${prefix}.paf $cigar_paf \\
$set_cigar_bam \\
$bam_output
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

18
modules/minimap2/align/meta.yml
View file

@ -29,6 +29,17 @@ input:
type: file type: file
description: | description: |
Reference database in FASTA format. Reference database in FASTA format.
- bam_format:
type: boolean
description: Specify that output should be in BAM format
- cigar_paf_format:
type: boolean
description: Specify that output CIGAR should be in PAF format
- cigar_bam:
type: boolean
description: |
Write CIGAR with >65535 ops at the CG tag. This is recommended when
doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)
output: output:
- meta: - meta:
type: map type: map
@ -39,9 +50,16 @@ output:
type: file type: file
description: Alignment in PAF format description: Alignment in PAF format
pattern: "*.paf" pattern: "*.paf"
- bam:
type: file
description: Alignment in BAM format
pattern: "*.bam"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@heuermh" - "@heuermh"
- "@sofstam"
- "@sateeshperi"
- "@jfy133"

39
modules/motus/downloaddb/main.nf Normal file
View file

@ -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
"""
}

39
modules/motus/downloaddb/meta.yml Normal file
View file

@ -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"

5
modules/phantompeakqualtools/main.nf
View file

@ -22,11 +22,12 @@ process PHANTOMPEAKQUALTOOLS {
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
RUN_SPP=`which run_spp.R` RUN_SPP=`which run_spp.R`
Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" $args2
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

18
modules/picard/addorreplacereadgroups/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.26.9" : null) conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)
@ -38,12 +38,12 @@ process PICARD_ADDORREPLACEREADGROUPS {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
--INPUT ${bam} \\ --INPUT ${bam} \\
--OUTPUT ${prefix}.bam \\ --OUTPUT ${prefix}.bam \\
-ID ${ID} \\ --RGID ${ID} \\
-LB ${LIBRARY} \\ --RGLB ${LIBRARY} \\
-PL ${PLATFORM} \\ --RGPL ${PLATFORM} \\
-PU ${BARCODE} \\ --RGPU ${BARCODE} \\
-SM ${SAMPLE} \\ --RGSM ${SAMPLE} \\
-CREATE_INDEX true --CREATE_INDEX true
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

10
modules/picard/cleansam/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_CLEANSAM {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.9" : null) conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)
@ -31,8 +31,8 @@ process PICARD_CLEANSAM {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
CleanSam \\ CleanSam \\
${args} \\ ${args} \\
-I ${bam} \\ --INPUT ${bam} \\
-O ${prefix}.bam --OUTPUT ${prefix}.bam
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

21
modules/picard/collecthsmetrics/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null) conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)
@ -15,8 +15,8 @@ process PICARD_COLLECTHSMETRICS {
path target_intervals path target_intervals
output: output:
tuple val(meta), path("*collecthsmetrics.txt"), emit: hs_metrics tuple val(meta), path("*_metrics") , emit: metrics
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
@ -38,10 +38,11 @@ process PICARD_COLLECTHSMETRICS {
CollectHsMetrics \\ CollectHsMetrics \\
$args \\ $args \\
$reference \\ $reference \\
-BAIT_INTERVALS $bait_intervals \\ --BAIT_INTERVALS $bait_intervals \\
-TARGET_INTERVALS $target_intervals \\ --TARGET_INTERVALS $target_intervals \\
-INPUT $bam \\ --INPUT $bam \\
-OUTPUT ${prefix}_collecthsmetrics.txt --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
@ -52,7 +53,7 @@ process PICARD_COLLECTHSMETRICS {
stub: stub:
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
touch ${prefix}_collecthsmetrics.txt touch ${prefix}.CollectHsMetrics.coverage_metrics
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

7
modules/picard/collecthsmetrics/meta.yml
View file

@ -57,10 +57,11 @@ output:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- hs_metrics: - metrics:
type: file type: file
description: The metrics file. description: Alignment metrics files generated by picard
pattern: "*_collecthsmetrics.txt" pattern: "*_{metrics}"
authors: authors:
- "@projectoriented" - "@projectoriented"
- "@matthdsm"

12
modules/picard/collectmultiplemetrics/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null) conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)
@ -33,9 +33,9 @@ process PICARD_COLLECTMULTIPLEMETRICS {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
CollectMultipleMetrics \\ CollectMultipleMetrics \\
$args \\ $args \\
INPUT=$bam \\ --INPUT $bam \\
OUTPUT=${prefix}.CollectMultipleMetrics \\ --OUTPUT ${prefix}.CollectMultipleMetrics \\
REFERENCE_SEQUENCE=$fasta --REFERENCE_SEQUENCE $fasta
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

15
modules/picard/collectwgsmetrics/main.nf
View file

@ -2,13 +2,13 @@ process PICARD_COLLECTWGSMETRICS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null) conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam), path(bai) tuple val(meta), path(bam)
path fasta path fasta
output: output:
@ -32,9 +32,10 @@ process PICARD_COLLECTWGSMETRICS {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
CollectWgsMetrics \\ CollectWgsMetrics \\
$args \\ $args \\
INPUT=$bam \\ --INPUT $bam \\
OUTPUT=${prefix}.CollectWgsMetrics.coverage_metrics \\ --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
REFERENCE_SEQUENCE=$fasta --REFERENCE_SEQUENCE $fasta
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

10
modules/picard/createsequencedictionary/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.9" : null) conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(fasta) tuple val(meta), path(fasta)
@ -31,8 +31,8 @@ process PICARD_CREATESEQUENCEDICTIONARY {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
CreateSequenceDictionary \\ CreateSequenceDictionary \\
$args \\ $args \\
R=$fasta \\ --REFERENCE $fasta \\
O=${prefix}.dict --OUTPUT ${prefix}.dict
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

6
modules/picard/crosscheckfingerprints/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_CROSSCHECKFINGERPRINTS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null) conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(input1) tuple val(meta), path(input1)

6
modules/picard/filtersamreads/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null) conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam), path(readlist) tuple val(meta), path(bam), path(readlist)

10
modules/picard/fixmateinformation/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_FIXMATEINFORMATION {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.26.9" : null) conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)
@ -31,8 +31,8 @@ process PICARD_FIXMATEINFORMATION {
picard \\ picard \\
FixMateInformation \\ FixMateInformation \\
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
-I ${bam} \\ --INPUT ${bam} \\
-O ${prefix}.bam \\ --OUTPUT ${prefix}.bam \\
--VALIDATION_STRINGENCY ${STRINGENCY} --VALIDATION_STRINGENCY ${STRINGENCY}
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml

16
modules/picard/liftovervcf/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_LIFTOVERVCF {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null) conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(input_vcf) tuple val(meta), path(input_vcf)
@ -35,11 +35,11 @@ process PICARD_LIFTOVERVCF {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
LiftoverVcf \\ LiftoverVcf \\
$args \\ $args \\
I=$input_vcf \\ --INPUT $input_vcf \\
O=${prefix}.lifted.vcf.gz \\ --OUTPUT ${prefix}.lifted.vcf.gz \\
CHAIN=$chain \\ --CHAIN $chain \\
REJECT=${prefix}.unlifted.vcf.gz \\ --REJECT ${prefix}.unlifted.vcf.gz \\
R=$fasta --REFERENCE_SEQUENCE $fasta
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

12
modules/picard/markduplicates/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null) conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)
@ -33,9 +33,9 @@ process PICARD_MARKDUPLICATES {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
MarkDuplicates \\ MarkDuplicates \\
$args \\ $args \\
I=$bam \\ --INPUT $bam \\
O=${prefix}.bam \\ --OUTPUT ${prefix}.bam \\
M=${prefix}.MarkDuplicates.metrics.txt --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

10
modules/picard/mergesamfiles/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null) conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bams) tuple val(meta), path(bams)
@ -33,8 +33,8 @@ process PICARD_MERGESAMFILES {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
MergeSamFiles \\ MergeSamFiles \\
$args \\ $args \\
${'INPUT='+bam_files.join(' INPUT=')} \\ ${'--INPUT '+bam_files.join(' --INPUT ')} \\
OUTPUT=${prefix}.bam --OUTPUT ${prefix}.bam
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
picard: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) picard: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)

6
modules/picard/sortsam/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_SORTSAM {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null) conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

10
modules/picard/sortvcf/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_SORTVCF {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null) conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcf) tuple val(meta), path(vcf)
@ -22,8 +22,8 @@ process PICARD_SORTVCF {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def seq_dict = sequence_dict ? "-SEQUENCE_DICTIONARY $sequence_dict" : "" def seq_dict = sequence_dict ? "--SEQUENCE_DICTIONARY $sequence_dict" : ""
def reference = reference ? "-REFERENCE_SEQUENCE $reference" : "" def reference = reference ? "--REFERENCE_SEQUENCE $reference" : ""
def avail_mem = 3 def avail_mem = 3
if (!task.memory) { if (!task.memory) {
log.info '[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' log.info '[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'

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