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Merge branch 'master' into maxquant

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Veit Schwämmle 2022-05-16 13:26:35 +02:00 committed by GitHub
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2
.editorconfig
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@ -8,5 +8,5 @@ trim_trailing_whitespace = true
indent_size = 4
indent_style = space
[*.{yml,yaml}]
[*.{md,yml,yaml}]
indent_size = 2

5
.github/CONTRIBUTING.md vendored
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@ -16,7 +16,9 @@ Contributions to the code are even more welcome ;)
If you'd like to write some code for nf-core/modules, the standard workflow is as follows:
1. Check that there isn't already an issue about your idea in the [nf-core/modules issues](https://github.com/nf-core/modules/issues) to avoid duplicating work
* If there isn't one already, please create one so that others know you're working on this
- If there isn't one already, please create one so that others know you're working on this
2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/modules repository](https://github.com/nf-core/modules) to your GitHub account
3. When adding a module file, follow the [guidelines](https://github.com/nf-core/modules#adding-a-new-module-file)
4. Ensure that [tests are working locally](https://github.com/nf-core/modules#running-tests-locally)
@ -40,7 +42,6 @@ These tests are run both with the latest available version of `Nextflow` and als
For further information/help, please consult the [nf-core/modules README](https://github.com/nf-core/modules) and don't hesitate to get in touch on the nf-core Slack [#modules](https://nfcore.slack.com/channels/modules) channel ([join our Slack here](https://nf-co.re/join/slack)).
### Images and figures
For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).

64
.github/ISSUE_TEMPLATE/bug_report.md vendored
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@ -1,64 +0,0 @@
---
name: Bug report
about: Report something that is broken or incorrect
title: "[BUG]"
---
<!--
# nf-core/module bug report
Hi there!
Thanks for telling us about a problem with the modules.
Please delete this text and anything that's not relevant from the template below:
-->
## Check Documentation
I have checked the following places for your error:
- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [ ] [nf-core/module documentation](https://github.com/nf-core/modules/blob/master/README.md)
## Description of the bug
<!-- A clear and concise description of what the bug is. -->
## Steps to reproduce
Steps to reproduce the behaviour:
1. Command line: <!-- [e.g. `nextflow run ...`] -->
2. See error: <!-- [Please provide your error message] -->
## Expected behaviour
<!-- A clear and concise description of what you expected to happen. -->
## Log files
Have you provided the following extra information/files:
- [ ] The command used to run the module
- [ ] The `.nextflow.log` file <!-- this is a hidden file in the directory where you launched the module -->
## System
- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
- Executor: <!-- [e.g. slurm, local, awsbatch...] -->
- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
- Version <!-- [e.g. 7, 10.13.6, 18.3...] -->
## Nextflow Installation
- Version: <!-- [e.g. 19.10.0] -->
## Container engine
- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
- version: <!-- [e.g. 1.0.0] -->
- Image tag: <!-- [e.g. nfcore/module:2.6] -->
## Additional context
<!-- Add any other context about the problem here. -->

52
.github/ISSUE_TEMPLATE/bug_report.yml vendored Normal file
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@ -0,0 +1,52 @@
name: Bug report
description: Report something that is broken or incorrect
labels: bug
body:
- type: checkboxes
attributes:
label: Have you checked the docs?
description: I have checked the following places for my error
options:
- label: "[nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)"
required: true
- label: "[nf-core modules documentation](https://nf-co.re/docs/contributing/modules)"
required: true
- type: textarea
id: description
attributes:
label: Description of the bug
description: A clear and concise description of what the bug is.
validations:
required: true
- type: textarea
id: command_used
attributes:
label: Command used and terminal output
description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
render: console
placeholder: |
$ nextflow run ...
Some output where something broke
- type: textarea
id: files
attributes:
label: Relevant files
description: |
Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
- type: textarea
id: system
attributes:
label: System information
description: |
* Nextflow version _(eg. 21.10.3)_
* Hardware _(eg. HPC, Desktop, Cloud)_
* Executor _(eg. slurm, local, awsbatch)_
* Container engine and version: _(e.g. Docker 1.0.0, Singularity, Conda, Podman, Shifter or Charliecloud)_
* OS and version: _(eg. CentOS Linux, macOS, Ubuntu 22.04)_
* Image tag: <!-- [e.g. nfcore/cellranger:2.6] -->

32
.github/ISSUE_TEMPLATE/feature_request.md vendored
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@ -1,32 +0,0 @@
---
name: Feature request
about: Suggest an idea for nf-core/modules
title: "[FEATURE]"
---
<!--
# nf-core/modules feature request
Hi there!
Thanks for suggesting a new feature for the modules!
Please delete this text and anything that's not relevant from the template below:
-->
## Is your feature request related to a problem? Please describe
<!-- A clear and concise description of what the problem is. -->
<!-- e.g. [I'm always frustrated when ...] -->
## Describe the solution you'd like
<!-- A clear and concise description of what you want to happen. -->
## Describe alternatives you've considered
<!-- A clear and concise description of any alternative solutions or features you've considered. -->
## Additional context
<!-- Add any other context about the feature request here. -->

32
.github/ISSUE_TEMPLATE/feature_request.yml vendored Normal file
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@ -0,0 +1,32 @@
name: Feature request
description: Suggest an idea for nf-core/modules
labels: feature
title: "[FEATURE]"
body:
- type: textarea
id: description
attributes:
label: Is your feature request related to a problem? Please describe
description: A clear and concise description of what the bug is.
placeholder: |
<!-- e.g. [I'm always frustrated when ...] -->
validations:
required: true
- type: textarea
id: solution
attributes:
label: Describe the solution you'd like
description: A clear and concise description of the solution you want to happen.
- type: textarea
id: alternatives
attributes:
label: Describe alternatives you've considered
description: A clear and concise description of any alternative solutions or features you've considered.
- type: textarea
id: additional_context
attributes:
label: Additional context
description: Add any other context about the feature request here.

26
.github/ISSUE_TEMPLATE/new_module.md vendored
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@ -1,26 +0,0 @@
---
name: New module
about: Suggest a new module for nf-core/modules
title: "new module: TOOL/SUBTOOL"
label: new module
---
<!--
# nf-core/modules new module suggestion
Hi there!
Thanks for suggesting a new module for the modules!
Please delete this text and anything that's not relevant from the template below:
Replace TOOL with the bioconda name for the tool in the following text, so that the link is functional.
Replace TOOL/SUBTOOL in the issue title so that it's understandable.
-->
I think it would be good to have a module for [TOOL](https://bioconda.github.io/recipes/TOOL/README.html)
- [ ] This module does not exist yet with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command
- [ ] There is no [open pull request](https://github.com/nf-core/modules/pulls) for this module
- [ ] There is no [open issue](https://github.com/nf-core/modules/issues) for this module
- [ ] If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module

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.github/ISSUE_TEMPLATE/new_module.yml vendored Normal file
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@ -0,0 +1,36 @@
name: New module
description: Suggest a new module for nf-core/modules
title: "new module: TOOL/SUBTOOL"
labels: new module
body:
- type: checkboxes
attributes:
label: Is there an existing module for this?
description: This module does not exist yet with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command
options:
- label: I have searched for the existing module
required: true
- type: checkboxes
attributes:
label: Is there an open PR for this?
description: There is no [open pull request](https://github.com/nf-core/modules/pulls) for this module
options:
- label: I have searched for existing PRs
required: true
- type: checkboxes
attributes:
label: Is there an open issue for this?
description: There is no [open issue](https://github.com/nf-core/modules/issues) for this module
options:
- label: I have searched for existing issues
required: true
- type: checkboxes
attributes:
label: Are you going to work on this?
description: If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module
options:
- label: If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module
required: false

6
.github/PULL_REQUEST_TEMPLATE.md vendored
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@ -27,6 +27,6 @@ Closes #XXX <!-- If this PR fixes an issue, please link it here! -->
- [ ] Add a resource `label`
- [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
- Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
- [ ] `PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd`
- [ ] `PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd`
- [ ] `PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd`
- [ ] `PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`
- [ ] `PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`
- [ ] `PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`

58
.github/workflows/code-linting.yml vendored
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@ -5,51 +5,31 @@ on:
pull_request:
branches: [master]
jobs:
Markdown:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-node@v1
with:
node-version: "10"
- name: Install markdownlint
run: npm install -g markdownlint-cli
- name: Run Markdownlint
run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.markdownlint.yml
EditorConfig:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-node@v1
with:
node-version: "10"
- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
- name: Run ECLint check
run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
YAML:
Prettier:
runs-on: ubuntu-latest
steps:
- name: Check out repository
uses: actions/checkout@v2
- name: Install NodeJS
uses: actions/setup-node@v1
with:
node-version: "10"
uses: actions/setup-node@v2
- name: Install yaml-lint
run: npm install -g yaml-lint
- name: Install Prettier
run: npm install -g prettier
- name: Run yaml-lint
run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yaml" -or -name "*.yml")
- name: Run Prettier --check
run: prettier --check .
EditorConfig:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-node@v2
- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
- name: Run ECLint check
run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)

10
.github/workflows/pytest-workflow.yml vendored
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@ -86,17 +86,13 @@ jobs:
# Test the module
- name: Run pytest-workflow
# only use one thread for pytest-workflow to avoid race condition on conda cache.
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
- name: Output log on failure
if: failure()
run: |
echo "======> log.out <======="
cat /home/runner/pytest_workflow_*/*/log.out
echo
echo
echo "======> log.err <======="
cat /home/runner/pytest_workflow_*/*/log.err
sudo apt install bat > /dev/null
batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
- name: Upload logs on failure
if: failure()

2
.gitpod.yml
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@ -4,7 +4,7 @@ vscode:
extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files
# - cssho.vscode-svgviewer # SVG viewer
- davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code
- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
- eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
- EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
- Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar

11
.markdownlint.yml
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@ -1,11 +0,0 @@
# Markdownlint configuration file
default: true
line-length: false
no-multiple-blanks: 0
blanks-around-headers: false
blanks-around-lists: false
header-increment: false
no-duplicate-header:
siblings_only: true
ul-indent:
indent: 4

16
.prettierignore Normal file
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@ -0,0 +1,16 @@
includes/Maven_Pro/
# gitignore
.nextflow*
work/
results/
test_output/
output/
.DS_Store
*.code-workspace
tests/data/
.screenrc
.*.sw?
__pycache__
*.pyo
*.pyc

1
.prettierrc.yml Normal file
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@ -0,0 +1 @@
printWidth: 120

2
README.md
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@ -133,7 +133,7 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
## Adding new modules
If you wish to contribute a new module, please see the documentation on the [nf-core website](https://nf-co.re/developers/adding_modules).
If you wish to contribute a new module, please see the documentation on the [nf-core website](https://nf-co.re/developers/modules#writing-a-new-module-reference).
> Please be kind to our code reviewers and submit one pull request per module :)

2
modules/abacas/meta.yml
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@ -14,7 +14,7 @@ tools:
documentation: http://abacas.sourceforge.net/documentation.html
tool_dev_url: None
doi: "10.1093/bioinformatics/btp347"
licence: ['GPL v2-or-later']
licence: ["GPL v2-or-later"]
input:
- meta:

34
modules/abricate/run/main.nf Normal file
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@ -0,0 +1,34 @@
process ABRICATE_RUN {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
input:
tuple val(meta), path(assembly)
output:
tuple val(meta), path("*.txt"), emit: report
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}"
"""
abricate \\
$assembly \\
$args \\
--threads $task.cpus > ${prefix}.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
END_VERSIONS
"""
}

43
modules/abricate/run/meta.yml Normal file
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@ -0,0 +1,43 @@
name: abricate_run
description: Screen assemblies for antimicrobial resistance against multiple databases
keywords:
- bacteria
- assembly
- antimicrobial reistance
tools:
- abricate:
description: Mass screening of contigs for antibiotic resistance genes
homepage: https://github.com/tseemann/abricate
documentation: https://github.com/tseemann/abricate
tool_dev_url: https://github.com/tseemann/abricate
doi: ""
licence: ["GPL v2", "GPL v2"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- assembly:
type: file
description: FASTA, GenBank or EMBL formatted file
pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- report:
type: file
description: Tab-delimited report of results
pattern: "*.{txt}"
authors:
- "@rpetit3"

33
modules/abricate/summary/main.nf Normal file
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@ -0,0 +1,33 @@
process ABRICATE_SUMMARY {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
input:
tuple val(meta), path(reports)
output:
tuple val(meta), path("*.txt"), emit: report
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}"
"""
abricate \\
--summary \\
$reports > ${prefix}.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
END_VERSIONS
"""
}

43
modules/abricate/summary/meta.yml Normal file
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@ -0,0 +1,43 @@
name: abricate_summary
description: Screen assemblies for antimicrobial resistance against multiple databases
keywords:
- bacteria
- assembly
- antimicrobial reistance
tools:
- abricate:
description: Mass screening of contigs for antibiotic resistance genes
homepage: https://github.com/tseemann/abricate
documentation: https://github.com/tseemann/abricate
tool_dev_url: https://github.com/tseemann/abricate
doi: ""
licence: ["GPL v2", "GPL v2"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- assembly:
type: file
description: FASTA, GenBank or EMBL formatted file
pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- summary:
type: file
description: Tab-delimited report of aggregated results
pattern: "*.{txt}"
authors:
- "@rpetit3"

72
modules/adapterremoval/main.nf
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@ -9,10 +9,16 @@ process ADAPTERREMOVAL {
input:
tuple val(meta), path(reads)
path(adapterlist)
output:
tuple val(meta), path('*.fastq.gz'), emit: reads
tuple val(meta), path('*.log') , emit: log
tuple val(meta), path("${prefix}.truncated.fastq.gz") , optional: true, emit: singles_truncated
tuple val(meta), path("${prefix}.discarded.fastq.gz") , optional: true, emit: discarded
tuple val(meta), path("${prefix}.pair{1,2}.truncated.fastq.gz") , optional: true, emit: paired_truncated
tuple val(meta), path("${prefix}.collapsed.fastq.gz") , optional: true, emit: collapsed
tuple val(meta), path("${prefix}.collapsed.truncated.fastq.gz") , optional: true, emit: collapsed_truncated
tuple val(meta), path("${prefix}.paired.fastq.gz") , optional: true, emit: paired_interleaved
tuple val(meta), path('*.settings') , emit: settings
path "versions.yml" , emit: versions
when:
@ -20,38 +26,29 @@ process ADAPTERREMOVAL {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def list = adapterlist ? "--adapter-list ${adapterlist}" : ""
prefix = task.ext.prefix ?: "${meta.id}"
if (meta.single_end) {
"""
AdapterRemoval \\
--file1 $reads \\
$args \\
--basename $prefix \\
--threads $task.cpus \\
--settings ${prefix}.log \\
--output1 ${prefix}.trimmed.fastq.gz \\
$adapterlist \\
--basename ${prefix} \\
--threads ${task.cpus} \\
--seed 42 \\
--gzip \\
--gzip
cat <<-END_VERSIONS > versions.yml
"${task.process}":
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
END_VERSIONS
"""
} else if (!meta.single_end && !meta.collapse) {
"""
AdapterRemoval \\
--file1 ${reads[0]} \\
--file2 ${reads[1]} \\
$args \\
--basename $prefix \\
--threads $task.cpus \\
--settings ${prefix}.log \\
--output1 ${prefix}.pair1.trimmed.fastq.gz \\
--output2 ${prefix}.pair2.trimmed.fastq.gz \\
--seed 42 \\
--gzip \\
ensure_fastq() {
if [ -f "\${1}" ]; then
mv "\${1}" "\${1::-3}.fastq.gz"
fi
}
ensure_fastq '${prefix}.truncated.gz'
ensure_fastq '${prefix}.discarded.gz'
cat <<-END_VERSIONS > versions.yml
"${task.process}":
@ -63,15 +60,28 @@ process ADAPTERREMOVAL {
AdapterRemoval \\
--file1 ${reads[0]} \\
--file2 ${reads[1]} \\
--collapse \\
$args \\
--basename $prefix \\
$adapterlist \\
--basename ${prefix} \\
--threads $task.cpus \\
--settings ${prefix}.log \\
--seed 42 \\
--gzip \\
--gzip
ensure_fastq() {
if [ -f "\${1}" ]; then
mv "\${1}" "\${1::-3}.fastq.gz"
fi
}
ensure_fastq '${prefix}.truncated.gz'
ensure_fastq '${prefix}.discarded.gz'
ensure_fastq '${prefix}.pair1.truncated.gz'
ensure_fastq '${prefix}.pair2.truncated.gz'
ensure_fastq '${prefix}.collapsed.gz'
ensure_fastq '${prefix}.collapsed.truncated.gz'
ensure_fastq '${prefix}.paired.gz'
cat *.collapsed.gz *.collapsed.truncated.gz > ${prefix}.merged.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")

76
modules/adapterremoval/meta.yml
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@ -10,22 +10,9 @@ tools:
description: The AdapterRemoval v2 tool for merging and clipping reads.
homepage: https://github.com/MikkelSchubert/adapterremoval
documentation: https://adapterremoval.readthedocs.io
licence: ['GPL v3']
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false, collapse:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
pattern: "*.{fq,fastq,fg.gz,fastq.gz}"
output:
- meta:
type: map
description: |
@ -34,13 +21,65 @@ output:
- reads:
type: file
description: |
List of input adapter trimmed FastQ files of size 1 or 2 for
single-end or collapsed data and paired-end data, respectively.
pattern: "*.{fastq.gz}"
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
- adapterlist:
type: file
description: Optional text file containing list of adapters to look for for removal
with one adapter per line. Otherwise will look for default adapters (see
AdapterRemoval man page), or can be modified to remove user-specified
adapters via ext.args.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- singles_truncated:
type: file
description: |
Adapter trimmed FastQ files of either single-end reads, or singleton
'orphaned' reads from merging of paired-end data (i.e., one of the pair
was lost due to filtering thresholds).
pattern: "*.truncated.fastq.gz"
- discarded:
type: file
description: |
Adapter trimmed FastQ files of reads that did not pass filtering
thresholds.
pattern: "*.discarded.fastq.gz"
- pair1_truncated:
type: file
description: |
Adapter trimmed R1 FastQ files of paired-end reads that did not merge
with their respective R2 pair due to long templates. The respective pair
is stored in 'pair2_truncated'.
pattern: "*.pair1.truncated.fastq.gz"
- pair2_truncated:
type: file
description: |
Adapter trimmed R2 FastQ files of paired-end reads that did not merge
with their respective R1 pair due to long templates. The respective pair
is stored in 'pair1_truncated'.
pattern: "*.pair2.truncated.fastq.gz"
- collapsed:
type: file
description: |
Collapsed FastQ of paired-end reads that successfully merged with their
respective R1 pair but were not trimmed.
pattern: "*.collapsed.fastq.gz"
- collapsed_truncated:
type: file
description: |
Collapsed FastQ of paired-end reads that successfully merged with their
respective R1 pair and were trimmed of adapter due to sufficient overlap.
pattern: "*.collapsed.truncated.fastq.gz"
- log:
type: file
description: AdapterRemoval log file
pattern: "*.log"
pattern: "*.settings"
- versions:
type: file
description: File containing software versions
@ -48,3 +87,4 @@ output:
authors:
- "@maxibor"
- "@jfy133"

38
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@ -0,0 +1,38 @@
def VERSION = '0.05'
process ADAPTERREMOVALFIXPREFIX {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2':
'quay.io/biocontainers/adapterremovalfixprefix:0.0.5--hdfd78af_2' }"
input:
tuple val(meta), path(fastq)
output:
tuple val(meta), path("*.fq.gz"), emit: fixed_fastq
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if ("$fastq" == "${prefix}.fq.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
"""
AdapterRemovalFixPrefix \\
$fastq \\
$args \\
| gzip > ${prefix}.fq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
adapterremovalfixprefix: $VERSION
END_VERSIONS
"""
}

43
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@ -0,0 +1,43 @@
name: adapterremovalfixprefix
description: Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.
keywords:
- adapterremoval
- fastq
- dedup
tools:
- adapterremovalfixprefix:
description: Fixes adapter removal prefixes to make sure no clashing read names are in the output.
homepage: https://github.com/apeltzer/AdapterRemovalFixPrefix
documentation: None
tool_dev_url: https://github.com/apeltzer/AdapterRemovalFixPrefix
doi: "10.1186/s13059-016-0918-z"
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fastq:
type: file
description: FASTQ file from AdapterRemoval2
pattern: "*.{fq.gz,fastq.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- fixed_fastq:
type: file
description: FASTQ file with fixed read prefixes for DeDup
pattern: "*.{fq.gz}"
authors:
- "@jfy133"

2
modules/agrvate/meta.yml
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@ -11,7 +11,7 @@ tools:
documentation: https://github.com/VishnuRaghuram94/AgrVATE
tool_dev_url: https://github.com/VishnuRaghuram94/AgrVATE
doi: ""
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

41
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@ -0,0 +1,41 @@
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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@ -0,0 +1,47 @@
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"

2
modules/amps/meta.yml
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@ -24,7 +24,7 @@ tools:
documentation: "https://github.com/keyfm/amps"
tool_dev_url: "https://github.com/keyfm/amps"
doi: "10.1186/s13059-019-1903-0"
licence: ['GPL >=3']
licence: ["GPL >=3"]
input:
- maltextract_results:

55
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@ -0,0 +1,55 @@
process AMRFINDERPLUS_RUN {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.23" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0':
'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }"
input:
tuple val(meta), path(fasta)
path db
output:
tuple val(meta), path("${prefix}.tsv") , emit: report
tuple val(meta), path("${prefix}-mutations.tsv"), emit: mutation_report, optional: true
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def is_compressed = fasta.getName().endsWith(".gz") ? true : false
prefix = task.ext.prefix ?: "${meta.id}"
organism_param = meta.containsKey("organism") ? "--organism ${meta.organism} --mutation_all ${prefix}-mutations.tsv" : ""
fasta_name = fasta.getName().replace(".gz", "")
fasta_param = "-n"
if (meta.containsKey("is_proteins")) {
if (meta.is_proteins) {
fasta_param = "-p"
}
}
"""
if [ "$is_compressed" == "true" ]; then
gzip -c -d $fasta > $fasta_name
fi
mkdir amrfinderdb
tar xzvf $db -C amrfinderdb
amrfinder \\
$fasta_param $fasta_name \\
$organism_param \\
$args \\
--database amrfinderdb \\
--threads $task.cpus > ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
amrfinderplus: \$(amrfinder --version)
END_VERSIONS
"""
}

51
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@ -0,0 +1,51 @@
name: amrfinderplus_run
description: Identify antimicrobial resistance in gene or protein sequences
keywords:
- bacteria
- fasta
- antibiotic resistance
tools:
- amrfinderplus:
description: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
homepage: https://github.com/ncbi/amr/wiki
documentation: https://github.com/ncbi/amr/wiki
tool_dev_url: https://github.com/ncbi/amr
doi: "10.1038/s41598-021-91456-0"
licence: ["Public Domain"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: Nucleotide or protein sequences in FASTA format
pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
- db:
type: file
description: A compressed tarball of the AMRFinderPlus database to query
pattern: "*.tar.gz"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- report:
type: file
description: AMRFinder+ final report
pattern: "*.tsv"
- mutation_report:
type: file
description: Report of organism-specific point-mutations
pattern: "*-mutations.tsv"
authors:
- "@rpetit3"

29
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@ -0,0 +1,29 @@
process AMRFINDERPLUS_UPDATE {
tag "update"
label 'process_low'
conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.23" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0':
'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }"
output:
path "amrfinderdb.tar.gz", emit: db
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
mkdir amrfinderdb
amrfinder_update -d amrfinderdb
tar czvf amrfinderdb.tar.gz -C \$(readlink amrfinderdb/latest) ./
cat <<-END_VERSIONS > versions.yml
"${task.process}":
amrfinderplus: \$(amrfinder --version)
END_VERSIONS
"""
}

37
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@ -0,0 +1,37 @@
name: amrfinderplus_update
description: Identify antimicrobial resistance in gene or protein sequences
keywords:
- bacteria
- fasta
- antibiotic resistance
tools:
- amrfinderplus:
description: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
homepage: https://github.com/ncbi/amr/wiki
documentation: https://github.com/ncbi/amr/wiki
tool_dev_url: https://github.com/ncbi/amr
doi: "10.1038/s41598-021-91456-0"
licence: ["Public Domain"]
input:
- input_not_required:
type: null
description: module does not have an input
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"
- db:
type: file
description: The latest AMRFinder+ database in a compressed tarball
pattern: "*.tar.gz"
authors:
- "@rpetit3"

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@ -0,0 +1,68 @@
process ANTISMASH_ANTISMASHLITE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
container "${ 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' }"
containerOptions {
workflow.containerEngine == 'singularity' ?
"-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
workflow.containerEngine == 'docker' ?
"-v \$PWD/$antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
''
}
input:
tuple val(meta), path(sequence_input)
path(databases)
path(antismash_dir) // Optional input: AntiSMASH installation folder. It is not needed for using this module with conda, but required for docker/singularity (see meta.yml).
path(gff)
output:
tuple val(meta), path("${prefix}/clusterblast/*_c*.txt") , optional: true, emit: clusterblast_file
tuple val(meta), path("${prefix}/{css,images,js}") , emit: html_accessory_files
tuple val(meta), path("${prefix}/knownclusterblast/region*/ctg*.html") , optional: true, emit: knownclusterblast_html
tuple val(meta), path("${prefix}/knownclusterblast/*_c*.txt") , optional: true, emit: knownclusterblast_txt
tuple val(meta), path("${prefix}/svg/clusterblast*.svg") , optional: true, emit: svg_files_clusterblast
tuple val(meta), path("${prefix}/svg/knownclusterblast*.svg") , optional: true, emit: svg_files_knownclusterblast
tuple val(meta), path("${prefix}/*.gbk") , emit: gbk_input
tuple val(meta), path("${prefix}/*.json") , emit: json_results
tuple val(meta), path("${prefix}/*.log") , emit: log
tuple val(meta), path("${prefix}/*.zip") , emit: zip
tuple val(meta), path("${prefix}/*region*.gbk") , emit: gbk_results
tuple val(meta), path("${prefix}/clusterblastoutput.txt") , optional: true, emit: clusterblastoutput
tuple val(meta), path("${prefix}/index.html") , emit: html
tuple val(meta), path("${prefix}/knownclusterblastoutput.txt") , optional: true, emit: knownclusterblastoutput
tuple val(meta), path("${prefix}/regions.js") , emit: json_sideloading
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
gff_flag = "--genefinding-gff3 ${gff}"
"""
## We specifically do not include annotations (--genefinding-tool none) as
## this should be run as a separate module for versioning purposes
antismash \\
$args \\
$gff_flag \\
-c $task.cpus \\
--output-dir $prefix \\
--genefinding-tool none \\
--logfile $prefix/${prefix}.log \\
--databases $databases \\
$sequence_input
cat <<-END_VERSIONS > versions.yml
"${task.process}":
antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
END_VERSIONS
"""
}

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@ -0,0 +1,128 @@
name: antismash_antismashlite
description: |
antiSMASH allows the rapid genome-wide identification, annotation
and analysis of secondary metabolite biosynthesis gene clusters.
keywords:
- secondary metabolites
- BGC
- biosynthetic gene cluster
- genome mining
- NRPS
- RiPP
- antibiotics
- prokaryotes
- bacteria
- eukaryotes
- fungi
- antismash
tools:
- antismashlite:
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:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- sequence_input:
type: file
description: nucleotide sequence file (annotated)
pattern: "*.{gbk, gb, gbff, genbank, embl, fasta, fna}"
- databases:
type: directory
description: downloaded AntiSMASH databases e.g. data/databases
pattern: "*/"
- antismash_dir:
type: directory
description: |
A local copy of an AntiSMASH installation folder. This is required when running with
docker and singularity (not required for conda), due to attempted 'modifications' of
files during database checks in the installation directory, something that cannot
be done in immutable docker/singularity containers. Therefore, a local installation
directory needs to be mounted (including all modified files from the downloading step)
to the container as a workaround.
pattern: "*/"
- gff:
type: file
pattern: "*.gff"
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"
- clusterblast_file:
type: file
description: Output of ClusterBlast algorithm
pattern: "clusterblast/*_c*.txt"
- html_accessory_files:
type: directory
description: Accessory files for the HTML output
pattern: "{css/,images/,js/}"
- knownclusterblast_html:
type: file
description: Tables with MIBiG hits in HTML format
pattern: "knownclusterblast/region*/ctg*.html"
- knownclusterblast_txt:
type: file
description: Tables with MIBiG hits
pattern: "knownclusterblast/*_c*.txt"
- svg_files_clusterblast:
type: file
description: SVG images showing the % identity of the aligned hits against their queries
pattern: "svg/clusterblast*.svg"
- svg_files_knownclusterblast:
type: file
description: SVG images showing the % identity of the aligned hits against their queries
pattern: "svg/knownclusterblast*.svg"
- gbk_input:
type: file
description: Nucleotide sequence and annotations in GenBank format; converted from input file
pattern: "*.gbk"
- json_results:
type: file
description: Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input)
pattern: "*.json"
- log:
type: file
description: Contains all the logging output that antiSMASH produced during its run
pattern: "*.log"
- zip:
type: file
description: Contains a compressed version of the output folder in zip format
pattern: "*.zip"
- gbk_results:
type: file
description: Nucleotide sequence and annotations in GenBank format; one file per antiSMASH hit
pattern: "*region*.gbk"
- clusterblastoutput:
type: file
description: Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm
pattern: "clusterblastoutput.txt"
- html:
type: file
description: Graphical web view of results in HTML format
patterN: "index.html"
- knownclusterblastoutput:
type: file
description: Raw BLAST output of known clusters of the MIBiG database
pattern: "knownclusterblastoutput.txt"
- json_sideloading:
type: file
description: Sideloaded annotations of protoclusters and/or subregions (see antiSMASH documentation "Annotation sideloading")
pattern: "regions.js"
authors:
- "@jasmezz"

56
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@ -0,0 +1,56 @@
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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@ -0,0 +1,60 @@
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"

32
modules/arriba/main.nf
View file

@ -2,15 +2,20 @@ process ARRIBA {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::arriba=2.1.0" : null)
conda (params.enable_conda ? "bioconda::arriba=2.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/arriba:2.1.0--h3198e80_1' :
'quay.io/biocontainers/arriba:2.1.0--h3198e80_1' }"
'https://depot.galaxyproject.org/singularity/arriba:2.2.1--hecb563c_2' :
'quay.io/biocontainers/arriba:2.2.1--hecb563c_2' }"
input:
tuple val(meta), path(bam)
path fasta
path gtf
path blacklist
path known_fusions
path structural_variants
path tags
path protein_domains
output:
tuple val(meta), path("*.fusions.tsv") , emit: fusions
@ -23,7 +28,12 @@ process ARRIBA {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def blacklist = (args.contains('-b')) ? '' : '-f blacklist'
def blacklist = blacklist ? "-b $blacklist" : "-f blacklist"
def known_fusions = known_fusions ? "-k $known_fusions" : ""
def structural_variants = structural_variants ? "-d $structual_variants" : ""
def tags = tags ? "-t $tags" : ""
def protein_domains = protein_domains ? "-p $protein_domains" : ""
"""
arriba \\
-x $bam \\
@ -32,6 +42,10 @@ process ARRIBA {
-o ${prefix}.fusions.tsv \\
-O ${prefix}.fusions.discarded.tsv \\
$blacklist \\
$known_fusions \\
$structural_variants \\
$tags \\
$protein_domains \\
$args
cat <<-END_VERSIONS > versions.yml
@ -39,4 +53,14 @@ process ARRIBA {
arriba: \$(arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
echo stub > ${prefix}.fusions.tsv
echo stub > ${prefix}.fusions.discarded.tsv
echo "${task.process}:" > versions.yml
echo ' arriba: 2.2.1' >> versions.yml
"""
}

24
modules/arriba/meta.yml
View file

@ -10,7 +10,7 @@ tools:
documentation: https://arriba.readthedocs.io/en/latest/
tool_dev_url: https://github.com/suhrig/arriba
doi: "10.1101/gr.257246.119"
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
@ -30,6 +30,26 @@ input:
type: file
description: Annotation GTF file
pattern: "*.{gtf}"
- blacklist:
type: file
description: Blacklist file
pattern: "*.{tsv}"
- known_fusions:
type: file
description: Known fusions file
pattern: "*.{tsv}"
- structural_variants:
type: file
description: Structural variants file
pattern: "*.{tsv}"
- tags:
type: file
description: Tags file
pattern: "*.{tsv}"
- protein_domains:
type: file
description: Protein domains file
pattern: "*.{gff3}"
output:
- meta:
@ -51,4 +71,4 @@ output:
pattern: "*.{fusions.discarded.tsv}"
authors:
- "@praveenraj2018"
- "@praveenraj2018,@rannick"

2
modules/artic/guppyplex/meta.yml
View file

@ -11,7 +11,7 @@ tools:
documentation: https://artic.readthedocs.io/en/latest/
tool_dev_url: https://github.com/artic-network/fieldbioinformatics
doi: ""
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

5
modules/artic/minion/main.nf
View file

@ -13,7 +13,8 @@ process ARTIC_MINION {
path sequencing_summary
path ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta")
path ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed")
path medaka_model
path medaka_model_file
val medaka_model_string
val scheme
val scheme_version
@ -44,7 +45,7 @@ process ARTIC_MINION {
if (args.tokenize().contains('--medaka')) {
fast5 = ""
summary = ""
model = file(medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $medaka_model"
model = medaka_model_file ? "--medaka-model ./$medaka_model_file" : "--medaka-model $medaka_model_string"
}
def hd5_plugin_path = task.ext.hd5_plugin_path ? "export HDF5_PLUGIN_PATH=" + task.ext.hd5_plugin_path : "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin"
"""

13
modules/artic/minion/meta.yml
View file

@ -12,7 +12,7 @@ tools:
documentation: https://artic.readthedocs.io/en/latest/
tool_dev_url: https://github.com/artic-network/fieldbioinformatics
doi: ""
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map
@ -42,11 +42,16 @@ input:
bed files containing coordinates of each primer in the scheme,
relative to the reference genome
pattern: "*.{scheme.bed}"
- medaka_model:
- medaka_model_file:
type: file
description: |
Medaka model to use (if option --medaka is set)
pattern: "*.*"
Medaka model file to use (if option --medaka is set)
pattern: "*.hdf5"
- medaka_model_string:
type: value
description: |
Medaka model string to use (if option --medaka is set)
pattern: "*"
- scheme:
type: value
description: Name of the primer scheme

155
modules/ascat/main.nf Normal file
View file

@ -0,0 +1,155 @@
process ASCAT {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount-4.3.0": null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0':
'quay.io/biocontainers/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0' }"
input:
tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor)
path(allele_files)
path(loci_files)
output:
tuple val(meta), path("*png"), emit: png
tuple val(meta), path("*cnvs.txt"), emit: cnvs
tuple val(meta), path("*purityploidy.txt"), emit: purityploidy
tuple val(meta), path("*segments.txt"), emit: segments
path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def gender = args.gender ? "$args.gender" : "NULL"
def genomeVersion = args.genomeVersion ? "$args.genomeVersion" : "NULL"
def purity = args.purity ? "$args.purity" : "NULL"
def ploidy = args.ploidy ? "$args.ploidy" : "NULL"
def gc_files = args.gc_files ? "$args.gc_files" : "NULL"
def minCounts_arg = args.minCounts ? ",minCounts = $args.minCounts" : ""
def chrom_names_arg = args.chrom_names ? ",chrom_names = $args.chrom_names" : ""
def min_base_qual_arg = args.min_base_qual ? ",min_base_qual = $args.min_base_qual" : ""
def min_map_qual_arg = args.min_map_qual ? ",min_map_qual = $args.min_map_qual" : ""
def ref_fasta_arg = args.ref_fasta ? ",ref.fasta = '$args.ref_fasta'" : ""
def skip_allele_counting_tumour_arg = args.skip_allele_counting_tumour ? ",skip_allele_counting_tumour = $args.skip_allele_counting_tumour" : ""
def skip_allele_counting_normal_arg = args.skip_allele_counting_normal ? ",skip_allele_counting_normal = $args.skip_allele_counting_normal" : ""
"""
#!/usr/bin/env Rscript
library(RColorBrewer)
library(ASCAT)
options(bitmapType='cairo')
#prepare from BAM files
ascat.prepareHTS(
tumourseqfile = "$input_tumor",
normalseqfile = "$input_normal",
tumourname = "Tumour",
normalname = "Normal",
allelecounter_exe = "alleleCounter",
alleles.prefix = "$allele_files",
loci.prefix = "$loci_files",
gender = "$gender",
genomeVersion = "$genomeVersion",
nthreads = $task.cpus
$minCounts_arg
$chrom_names_arg
$min_base_qual_arg
$min_map_qual_arg
$ref_fasta_arg
$skip_allele_counting_tumour_arg
$skip_allele_counting_normal_arg
)
#Load the data
ascat.bc = ascat.loadData(
Tumor_LogR_file = "Tumour_tumourLogR.txt",
Tumor_BAF_file = "Tumour_normalBAF.txt",
Germline_LogR_file = "Tumour_normalLogR.txt",
Germline_BAF_file = "Tumour_normalBAF.txt",
genomeVersion = "$genomeVersion",
gender = "$gender"
)
#optional GC wave correction
if(!is.null($gc_files)){
ascat.bc = ascat.GCcorrect(ascat.bc, $gc_files)
}
#Plot the raw data
ascat.plotRawData(ascat.bc)
#Segment the data
ascat.bc = ascat.aspcf(ascat.bc)
#Plot the segmented data
ascat.plotSegmentedData(ascat.bc)
#Run ASCAT to fit every tumor to a model, inferring ploidy, normal cell contamination, and discrete copy numbers
#If psi and rho are manually set:
if (!is.null($purity) && !is.null($ploidy)){
ascat.output <- ascat.runAscat(ascat.bc, gamma=1, rho_manual=$purity, psi_manual=$ploidy)
} else if(!is.null($purity) && is.null($ploidy)){
ascat.output <- ascat.runAscat(ascat.bc, gamma=1, rho_manual=$purity)
} else if(!is.null($ploidy) && is.null($purity)){
ascat.output <- ascat.runAscat(ascat.bc, gamma=1, psi_manual=$ploidy)
} else {
ascat.output <- ascat.runAscat(ascat.bc, gamma=1)
}
#Write out segmented regions (including regions with one copy of each allele)
write.table(ascat.output[["segments"]], file=paste0("$prefix", ".segments.txt"), sep="\t", quote=F, row.names=F)
#Write out CNVs in bed format
cnvs=ascat.output[["segments"]][2:6]
write.table(cnvs, file=paste0("$prefix",".cnvs.txt"), sep="\t", quote=F, row.names=F, col.names=T)
#Write out purity and ploidy info
summary <- tryCatch({
matrix(c(ascat.output[["aberrantcellfraction"]], ascat.output[["ploidy"]]), ncol=2, byrow=TRUE)}, error = function(err) {
# error handler picks up where error was generated
print(paste("Could not find optimal solution: ",err))
return(matrix(c(0,0),nrow=1,ncol=2,byrow = TRUE))
}
)
colnames(summary) <- c("AberrantCellFraction","Ploidy")
write.table(summary, file=paste0("$prefix",".purityploidy.txt"), sep="\t", quote=F, row.names=F, col.names=T)
#version export. Have to hardcode process name and software name because
#won't run inside an R-block
version_file_path="versions.yml"
f <- file(version_file_path,"w")
writeLines("ASCAT:", f)
writeLines(" ascat: 3.0.0",f)
close(f)
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
echo stub > ${prefix}.cnvs.txt
echo stub > ${prefix}.purityploidy.txt
echo stub > ${prefix}.segments.txt
echo stub > Tumour.ASCATprofile.png
echo stub > Tumour.ASPCF.png
echo stub > Tumour.germline.png
echo stub > Tumour.rawprofile.png
echo stub > Tumour.sunrise.png
echo stub > Tumour.tumour.png
echo 'ASCAT:' > versions.yml
echo ' ascat: 3.0.0' >> versions.yml
"""
}

92
modules/ascat/meta.yml Normal file
View file

@ -0,0 +1,92 @@
name: ascat
description: copy number profiles of tumour cells.
keywords:
- sort
tools:
- ascat:
description: ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy. ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell), expressed as multiples of haploid genomes from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome).
homepage: None
documentation: None
tool_dev_url: https://github.com/Crick-CancerGenomics/ascat
doi: "10.1093/bioinformatics/btaa538"
licence: ["GPL v3"]
input:
- args:
type: map
description: |
Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes. (optional) parameters can be removed from the map, if they are not set. For default values, please check the documentation above.
```
{
[
"gender": "XX",
"genomeVersion": "hg19"
"purity": (optional),
"ploidy": (optional),
"gc_files": (optional),
"minCounts": (optional),
"chrom_names": (optional),
"min_base_qual": (optional),
"min_map_qual": (optional),
"ref_fasta": (optional),
"skip_allele_counting_tumour": (optional),
"skip_allele_counting_normal": (optional)
]
}
```
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input_normal:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- index_normal:
type: file
description: index for normal_bam
pattern: "*.{bai}"
- input_tumor:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- index_tumor:
type: file
description: index for tumor_bam
pattern: "*.{bai}"
- allele_files:
type: file
description: allele files for ASCAT. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS
- loci_files:
type: file
description: loci files for ASCAT. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS
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"
- png:
type: file
description: ASCAT plots
pattern: "*.{png}"
- purityploidy:
type: file
description: purity and ploidy data
pattern: "*.purityploidy.txt"
- segments:
type: file
description: segments data
pattern: "*.segments.txt"
authors:
- "@aasNGC"
- "@lassefolkersen"
- "@FriederikeHanssen"
- "@maxulysse"

2
modules/assemblyscan/meta.yml
View file

@ -10,7 +10,7 @@ tools:
documentation: https://github.com/rpetit3/assembly-scan
tool_dev_url: https://github.com/rpetit3/assembly-scan
doi: ""
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

2
modules/ataqv/ataqv/meta.yml
View file

@ -9,7 +9,7 @@ tools:
documentation: https://github.com/ParkerLab/ataqv/blob/master/README.rst
tool_dev_url: https://github.com/ParkerLab/ataqv
doi: "https://doi.org/10.1016/j.cels.2020.02.009"
licence: ['GPL v3']
licence: ["GPL v3"]
input:
- meta:

8
modules/bakta/main.nf
View file

@ -2,10 +2,10 @@ process BAKTA {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bakta=1.2.2" : null)
conda (params.enable_conda ? "bioconda::bakta=1.4.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bakta:1.2.2--pyhdfd78af_0' :
'quay.io/biocontainers/bakta:1.2.2--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/bakta:1.4.0--pyhdfd78af_1' :
'quay.io/biocontainers/bakta:1.4.0--pyhdfd78af_1' }"
input:
tuple val(meta), path(fasta)
@ -23,6 +23,7 @@ process BAKTA {
tuple val(meta), path("${prefix}.hypotheticals.tsv"), emit: hypotheticals_tsv
tuple val(meta), path("${prefix}.hypotheticals.faa"), emit: hypotheticals_faa
tuple val(meta), path("${prefix}.tsv") , emit: tsv
tuple val(meta), path("${prefix}.txt") , emit: txt
path "versions.yml" , emit: versions
when:
@ -61,6 +62,7 @@ process BAKTA {
touch ${prefix}.hypotheticals.tsv
touch ${prefix}.hypotheticals.faa
touch ${prefix}.tsv
touch ${prefix}.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":

17
modules/bakta/meta.yml
View file

@ -1,17 +1,17 @@
name: bakta
description: Rapid annotation of bacterial genomes & plasmids.
description: Annotation of bacterial genomes (isolates, MAGs) and plasmids
keywords:
- annotation
- fasta
- prokaryote
- bacteria
tools:
- bakta:
description: Rapid & standardized annotation of bacterial genomes & plasmids.
description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.
homepage: https://github.com/oschwengers/bakta
documentation: https://github.com/oschwengers/bakta
tool_dev_url: https://github.com/oschwengers/bakta
doi: "10.1099/mgen.0.000685"
licence: ['GPL v3']
licence: ["GPL v3"]
input:
- meta:
@ -29,7 +29,7 @@ input:
Path to the Bakta database
- proteins:
type: file
description: FASTA file of trusted proteins to first annotate from (optional)
description: FASTA/GenBank file of trusted proteins to first annotate from (optional)
- prodigal_tf:
type: file
description: Training file to use for Prodigal (optional)
@ -44,6 +44,10 @@ output:
type: file
description: File containing software versions
pattern: "versions.yml"
- txt:
type: file
description: genome statistics and annotation summary
pattern: "*.txt"
- tsv:
type: file
description: annotations as simple human readble tab separated values
@ -74,7 +78,7 @@ output:
pattern: "*.ffn"
- hypotheticals_tsv:
type: file
description: further information on hypothetical protein CDS as simple human readble tab separated values
description: additional information on hypothetical protein CDS as simple human readble tab separated values
pattern: "*.hypotheticals.tsv"
- hypotheticals_faa:
type: file
@ -83,3 +87,4 @@ output:
authors:
- "@rpetit3"
- "@oschwengers"

2
modules/bamaligncleaner/meta.yml
View file

@ -8,7 +8,7 @@ tools:
homepage: https://github.com/maxibor/bamAlignCleaner
documentation: https://github.com/maxibor/bamAlignCleaner
tool_dev_url: https://github.com/maxibor/bamAlignCleaner
licence: ['GPL v3']
licence: ["GPL v3"]
input:
- meta:

5
modules/bamcmp/meta.yml
View file

@ -10,14 +10,15 @@ keywords:
tools:
- bamcmp:
description: Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped,
description:
Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped,
sorted bam files supplied to the tool. It is highly recommended to use the "-s as" option not the "-s mapq" option, else
reads which multimap to the contamination genome will be spuriously kept.
homepage: https://github.com/CRUKMI-ComputationalBiology/bamcmp
documentation: https://github.com/CRUKMI-ComputationalBiology/bamcmp
tool_dev_url: https://github.com/CRUKMI-ComputationalBiology/bamcmp
doi: "10.1158/1541-7786.MCR-16-0431"
licence: ['GPL v3']
licence: ["GPL v3"]
input:
- meta:

2
modules/bamtools/convert/meta.yml
View file

@ -19,7 +19,7 @@ tools:
documentation: https://github.com/pezmaster31/bamtools/wiki
tool_dev_url: http://github.com/pezmaster31/bamtools
doi: ""
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

12
modules/bamtools/split/main.nf
View file

@ -2,10 +2,10 @@ process BAMTOOLS_SPLIT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0' :
'quay.io/biocontainers/bamtools:2.5.2--hd03093a_0' }"
input:
tuple val(meta), path(bam)
@ -20,10 +20,14 @@ process BAMTOOLS_SPLIT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def input_list = bam.collect{"-in $it"}.join(' ')
"""
bamtools \\
merge \\
$input_list \\
| bamtools \\
split \\
-in $bam \\
-stub $prefix \\
$args
cat <<-END_VERSIONS > versions.yml

5
modules/bamtools/split/meta.yml
View file

@ -13,7 +13,7 @@ tools:
documentation: https://github.com/pezmaster31/bamtools/wiki
tool_dev_url: http://github.com/pezmaster31/bamtools
doi: ""
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
@ -23,7 +23,7 @@ input:
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: A BAM file to split
description: A list of one or more BAM files to merge and then split
pattern: "*.bam"
output:
@ -43,3 +43,4 @@ output:
authors:
- "@sguizard"
- "@matthdsm"

2
modules/bamutil/trimbam/meta.yml
View file

@ -13,7 +13,7 @@ tools:
documentation: https://genome.sph.umich.edu/wiki/BamUtil:_trimBam
tool_dev_url: https://github.com/statgen/bamUtil
doi: "10.1101/gr.176552.114"
licence: ['GPL v3']
licence: ["GPL v3"]
input:
- meta:

2
modules/bandage/image/meta.yml
View file

@ -11,7 +11,7 @@ tools:
Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
homepage: https://github.com/rrwick/Bandage
documentation: https://github.com/rrwick/Bandage
licence: ['GPL-3.0-or-later']
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map

6
modules/bbmap/align/main.nf
View file

@ -2,10 +2,10 @@ process BBMAP_ALIGN {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.13 pigz=2.6" : null)
conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' :
'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' :
'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' }"
input:
tuple val(meta), path(fastq)

2
modules/bbmap/align/meta.yml
View file

@ -13,7 +13,7 @@ tools:
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
tool_dev_url: None
doi: ""
licence: ['UC-LBL license (see package)']
licence: ["UC-LBL license (see package)"]
input:
- meta:

2
modules/bbmap/bbduk/meta.yml
View file

@ -11,7 +11,7 @@ tools:
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
tool_dev_url: None
doi: ""
licence: ['UC-LBL license (see package)']
licence: ["UC-LBL license (see package)"]
input:
- meta:

2
modules/bbmap/bbsplit/meta.yml
View file

@ -12,7 +12,7 @@ tools:
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
tool_dev_url: None
doi: ""
licence: ['UC-LBL license (see package)']
licence: ["UC-LBL license (see package)"]
input:
- meta:

2
modules/bbmap/index/meta.yml
View file

@ -11,7 +11,7 @@ tools:
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
tool_dev_url: None
doi: ""
licence: ['UC-LBL license (see package)']
licence: ["UC-LBL license (see package)"]
input:
- fasta:

39
modules/bbmap/pileup/main.nf Normal file
View file

@ -0,0 +1,39 @@
process BBMAP_PILEUP {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' :
'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.stats.txt"), emit: covstats
tuple val(meta), path("*.hist.txt") , emit: hist
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
pileup.sh \\
-Xmx${task.memory.toGiga()}g \\
in=${bam} \\
out=${prefix}.coverage.stats.txt \\
hist=${prefix}.coverage.hist.txt \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bbmap: \$(bbversion.sh)
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
}

47
modules/bbmap/pileup/meta.yml Normal file
View file

@ -0,0 +1,47 @@
name: "bbmap_pileup"
description: Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file.
keywords:
- fasta
- genome
- coverage
tools:
- bbmap:
description: BBMap is a short read aligner, as well as various other bioinformatic tools.
homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
tool_dev_url: "https://github.com/BioInfoTools/BBMap/blob/master/sh/pileup.sh"
doi: ""
licence: ["UC-LBL license (see package)"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- stats:
type: file
description: Per-scaffold coverage info
pattern: "*.stats.txt"
- hist:
type: file
description: "Histogram of # occurrences of each depth level"
pattern: "*.hist.txt"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@Emiller88"

42
modules/bcftools/annotate/main.nf Normal file
View file

@ -0,0 +1,42 @@
process BCFTOOLS_ANNOTATE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::bcftools=1.15" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.15--haf5b3da_0':
'quay.io/biocontainers/bcftools:1.15--haf5b3da_0' }"
input:
tuple val(meta), path(input)
output:
tuple val(meta), path("*_annotated.vcf.gz"), optional:true , emit: vcf
tuple val(meta), path("*_annotated.bcf") , optional:true , emit: bcf
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 matcher = input ==~ /\S+\.*vcf\.\S*/
def output_suffix = matcher ? "vcf.gz" : "bcf"
def output_type_compressed = matcher ? "z" : "b"
"""
bcftools \\
annotate \\
$args \\
--output ${prefix}_annotated.${output_suffix} \\
--output-type $output_type_compressed \\
--threads $task.cpus \\
$input
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' )
END_VERSIONS
"""
}

45
modules/bcftools/annotate/meta.yml Normal file
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@ -0,0 +1,45 @@
name: bcftools_annotate
description: Add or remove annotations.
keywords:
- bcftools
- annotate
- vcf
- remove
- add
tools:
- annotate:
description: Add or remove annotations.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: https://samtools.github.io/bcftools/bcftools.html#annotate
doi: 10.1093/bioinformatics/btp352
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: files
description: Query VCF or BCF file, can be either uncompressed or compressed
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- vcf:
type: file
description: Compressed annotated VCF file
pattern: "*_annotated.vcf.gz"
- bcf:
type: file
description: Compressed annotated BCF file
pattern: "*_annotated.bcf"
authors:
- "@projectoriented"

2
modules/bcftools/concat/meta.yml
View file

@ -13,7 +13,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bcftools/consensus/meta.yml
View file

@ -11,7 +11,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bcftools/filter/meta.yml
View file

@ -11,7 +11,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bcftools/index/meta.yml
View file

@ -13,7 +13,7 @@ tools:
documentation: https://samtools.github.io/bcftools/howtos/index.html
tool_dev_url: https://github.com/samtools/bcftools
doi: "10.1093/gigascience/giab008"
licence: ['MIT', 'GPL-3.0-or-later']
licence: ["MIT", "GPL-3.0-or-later"]
input:
- meta:

2
modules/bcftools/isec/meta.yml
View file

@ -13,7 +13,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bcftools/merge/meta.yml
View file

@ -11,7 +11,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bcftools/mpileup/meta.yml
View file

@ -11,7 +11,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

11
modules/bcftools/norm/main.nf
View file

@ -34,4 +34,15 @@ process BCFTOOLS_NORM {
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
}

2
modules/bcftools/norm/meta.yml
View file

@ -12,7 +12,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bcftools/query/meta.yml
View file

@ -12,7 +12,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bcftools/reheader/meta.yml
View file

@ -11,7 +11,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://samtools.github.io/bcftools/bcftools.html#reheader
doi: 10.1093/gigascience/giab008
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

2
modules/bcftools/sort/meta.yml
View file

@ -11,7 +11,7 @@ tools:
documentation: http://www.htslib.org/doc/bcftools.html
tool_dev_url: https://github.com/samtools/bcftools
doi: "10.1093/bioinformatics/btp352"
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

2
modules/bcftools/stats/meta.yml
View file

@ -12,7 +12,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

11
modules/bcftools/view/main.nf
View file

@ -41,4 +41,15 @@ process BCFTOOLS_VIEW {
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
}

2
modules/bcftools/view/meta.yml
View file

@ -13,7 +13,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bclconvert/.gitignore vendored Normal file
View file

@ -0,0 +1,2 @@
bcl-convert
*.rpm

15
modules/bclconvert/Dockerfile Normal file
View file

@ -0,0 +1,15 @@
# 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
View file

@ -0,0 +1,30 @@
ILLUMINA END-USER SOFTWARE LICENSE AGREEMENT
IMPORTANT-READ CAREFULLY. THIS IS A LICENSE AGREEMENT THAT YOU ARE REQUIRED TO ACCEPT BEFORE, DOWNLOADING, INSTALLING AND USING ANY SOFTWARE MADE AVAILABLE FROM THE ILLUMINA SUPPORT CENTER (https://support.illumina.com).
CAREFULLY READ ALL THE TERMS AND CONDITIONS OF THIS LICENSE AGREEMENT BEFORE PROCEEDING WITH DOWNLOADING, INSTALLING, AND/OR USING THE SOFTWARE. YOU ARE NOT PERMITTED TO DOWNLOAD, INSTALL, AND/OR USE THE SOFTWARE UNTIL YOU HAVE AGREED TO BE BOUND BY ALL OF THE TERMS AND CONDITIONS OF THIS LICENSE AGREEMENT. YOU REPRESENT AND WARRANT THAT YOU ARE DULY AUTHORIZED TO ACCEPT THE TERMS AND CONDITIONS OF THIS LICENSE AGREEMENT ON BEHALF OF YOUR EMPLOYER.
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Governing Law. This Agreement WILL be governed by and construed in accordance with the laws of the state of California, USA, without regard to its conflicts of laws principles, and independent of where a suit or action hereunder may be filed.
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Contact. Any questions regarding legal rights, duties, obligations, or restrictions associated with the software hereunder should be directed to Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, Attention: Legal Department, Phone: (858) 202-4500, Fax: (858) 202-4599, web site: www.illumina.com <http://www.illumina.com>.
Third Party Components. The Software may include third party software (“Third Party Programs”). Some of the Third Party Programs are available under open source or free software licenses. The License Agreement accompanying the Licensed Software does not alter any rights or obligations Licensee may have under those open source or free software licenses. The licenses that govern the terms and conditions of use of the Third Party Programs included in the Licensed Software are provided in the READ ME provided with the Software. The READ ME also contains copyright statements for the various open source software components (or portions thereof) that are distributed with the Licensed Software.
END OF END-USER SOFTWARE LICENSE AGREEMENT.

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# 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>
```

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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
"""
}

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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"

2
modules/bedtools/bamtobed/meta.yml
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@ -8,7 +8,7 @@ tools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bedtools/complement/meta.yml
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@ -8,7 +8,7 @@ tools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bedtools/genomecov/meta.yml
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@ -9,7 +9,7 @@ tools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bedtools/getfasta/meta.yml
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@ -9,7 +9,7 @@ tools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
licence: ['MIT']
licence: ["MIT"]
input:
- bed:
type: file

2
modules/bedtools/intersect/meta.yml
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@ -8,7 +8,7 @@ tools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bedtools/makewindows/meta.yml
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@ -11,7 +11,7 @@ tools:
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html
tool_dev_url: None
doi: "10.1093/bioinformatics/btq033"
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bedtools/maskfasta/meta.yml
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@ -9,7 +9,7 @@ tools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bedtools/merge/meta.yml
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@ -8,7 +8,7 @@ tools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bedtools/slop/meta.yml
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@ -8,7 +8,7 @@ tools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bedtools/sort/meta.yml
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@ -8,7 +8,7 @@ tools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bedtools/subtract/meta.yml
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@ -10,7 +10,7 @@ tools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

36
modules/biobambam/bammarkduplicates2/main.nf Normal file
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process BIOBAMBAM_BAMMARKDUPLICATES2 {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1' : 'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1'}"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.bam") , emit: bam
tuple val(meta), path("*.metrics.txt"), 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}"
"""
bammarkduplicates2 \\
$args \\
I=$bam \\
O=${prefix}.bam \\
M=${prefix}.metrics.txt \\
tmpfile=$prefix \\
markthreads=$task.cpus
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bammarkduplicates2: \$(echo \$(bammarkduplicates2 --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
END_VERSIONS
"""
}

44
modules/biobambam/bammarkduplicates2/meta.yml Normal file
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@ -0,0 +1,44 @@
name: biobambam_bammarkduplicates2
description: Locate and tag duplicate reads in a BAM file
keywords:
- markduplicates
- bam
- cram
tools:
- biobambam:
description: |
biobambam is a set of tools for early stage alignment file processing.
homepage: https://gitlab.com/german.tischler/biobambam2
documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md
doi: 10.1186/1751-0473-9-13
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM file
pattern: "*.{bam,cram}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file with duplicate reads marked/removed
pattern: "*.{bam}"
- metrics:
type: file
description: Duplicate metrics file generated by biobambam
pattern: "*.{metrics.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@muffato"

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modules/biobambam/bamsormadup/main.nf Normal file
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process BIOBAMBAM_BAMSORMADUP {
tag "$meta.id"
label "process_medium"
conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1' : 'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1'}"
input:
tuple val(meta), path(bams)
path(fasta)
output:
tuple val(meta), path("*.{bam,cram}") ,emit: bam
tuple val(meta), path("*.bam.bai") ,optional:true, emit: bam_index
tuple val(meta), path("*.metrics.txt") ,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 ?: "${meta.id}"
def suffix = args.contains("outputformat=cram") ? "cram" : "bam"
def input_string = bams.join(" I=")
if (args.contains("outputformat=cram") && reference == null) error "Reference required for CRAM output."
"""
bamcat \\
I=${input_string} \\
level=0 \\
| bamsormadup \\
$args \\
M=${prefix}.metrics.txt \\
tmpfile=$prefix \\
threads=$task.cpus \\
> ${prefix}.${suffix}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bamcat: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
bamsormadup: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
END_VERSIONS
"""
}

52
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name: biobambam_bamsormadup
description: Parallel sorting and duplicate marking
keywords:
- markduplicates
- sort
- bam
- cram
tools:
- biobambam:
description: |
biobambam is a set of tools for early stage alignment file processing.
homepage: https://gitlab.com/german.tischler/biobambam2
documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md
doi: 10.1186/1751-0473-9-13
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bams:
type: file
description: List containing 1 or more bam files
- fasta:
type: file
description: Reference genome in FASTA format (optional)
pattern: "*.{fa,fasta}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM file with duplicate reads marked/removed
pattern: "*.{bam,cram}"
- bam_index:
type: file
description: BAM index file
pattern: "*.{bai}"
- metrics:
type: file
description: Duplicate metrics file generated by biobambam
pattern: "*.{metrics.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@matthdsm"

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