mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
Merge remote-tracking branch 'nf-core/master'
This commit is contained in:
Chris Cheshire
commit
4bb0423a1d
1613 changed files with 30251 additions and 6880 deletions
|
|
@ -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
5
.github/CONTRIBUTING.md
vendored
|
|
@ -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
64
.github/ISSUE_TEMPLATE/bug_report.md
vendored
|
|
@ -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
52
.github/ISSUE_TEMPLATE/bug_report.yml
vendored
Normal file
|
|
@ -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
32
.github/ISSUE_TEMPLATE/feature_request.md
vendored
|
|
@ -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
32
.github/ISSUE_TEMPLATE/feature_request.yml
vendored
Normal file
|
|
@ -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
26
.github/ISSUE_TEMPLATE/new_module.md
vendored
|
|
@ -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
|
||||
36
.github/ISSUE_TEMPLATE/new_module.yml
vendored
Normal file
36
.github/ISSUE_TEMPLATE/new_module.yml
vendored
Normal file
|
|
@ -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
6
.github/PULL_REQUEST_TEMPLATE.md
vendored
|
|
@ -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
58
.github/workflows/code-linting.yml
vendored
|
|
@ -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 $(git ls-files | grep -v test)
|
||||
|
|
|
|||
10
.github/workflows/pytest-workflow.yml
vendored
10
.github/workflows/pytest-workflow.yml
vendored
|
|
@ -86,17 +86,13 @@ jobs:
|
|||
# Test the module
|
||||
- name: Run pytest-workflow
|
||||
# only use one thread for pytest-workflow to avoid race condition on conda cache.
|
||||
run: TMPDIR=~ PROFILE=${{ 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()
|
||||
|
|
|
|||
22
.gitpod.yml
22
.gitpod.yml
|
|
@ -1,10 +1,14 @@
|
|||
# List the start up tasks. Learn more https://www.gitpod.io/docs/config-start-tasks/
|
||||
tasks:
|
||||
- name: Install Nextflow
|
||||
init: |
|
||||
curl -s https://get.nextflow.io | bash
|
||||
sudo mv nextflow /usr/local/bin
|
||||
image: nfcore/gitpod:latest
|
||||
|
||||
- name: Install pytest-workflow
|
||||
init: |
|
||||
pip install pytest-workflow
|
||||
vscode:
|
||||
extensions: # based on nf-core.nf-core-extensionpack
|
||||
- codezombiech.gitignore # Language support for .gitignore files
|
||||
# - cssho.vscode-svgviewer # SVG viewer
|
||||
- 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
|
||||
- mechatroner.rainbow-csv # Highlight columns in csv files in different colors
|
||||
# - nextflow.nextflow # Nextflow syntax highlighting
|
||||
- oderwat.indent-rainbow # Highlight indentation level
|
||||
- streetsidesoftware.code-spell-checker # Spelling checker for source code
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
@ -1,3 +1,4 @@
|
|||
repository_type: modules
|
||||
bump-versions:
|
||||
rseqc/junctionannotation: False
|
||||
rseqc/bamstat: False
|
||||
|
|
|
|||
16
.prettierignore
Normal file
16
.prettierignore
Normal file
|
|
@ -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
1
.prettierrc.yml
Normal file
|
|
@ -0,0 +1 @@
|
|||
printWidth: 120
|
||||
144
README.md
144
README.md
|
|
@ -31,109 +31,109 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
|
|||
1. Install the latest version of [`nf-core/tools`](https://github.com/nf-core/tools#installation) (`>=2.0`)
|
||||
2. List the available modules:
|
||||
|
||||
```console
|
||||
$ nf-core modules list remote
|
||||
```console
|
||||
$ nf-core modules list remote
|
||||
|
||||
,--./,-.
|
||||
___ __ __ __ ___ /,-._.--~\
|
||||
|\ | |__ __ / ` / \ |__) |__ } {
|
||||
| \| | \__, \__/ | \ |___ \`-._,-`-,
|
||||
`._,._,'
|
||||
,--./,-.
|
||||
___ __ __ __ ___ /,-._.--~\
|
||||
|\ | |__ __ / ` / \ |__) |__ } {
|
||||
| \| | \__, \__/ | \ |___ \`-._,-`-,
|
||||
`._,._,'
|
||||
|
||||
nf-core/tools version 2.0
|
||||
nf-core/tools version 2.0
|
||||
|
||||
INFO Modules available from nf-core/modules (master): pipeline_modules.py:164
|
||||
INFO Modules available from nf-core/modules (master): pipeline_modules.py:164
|
||||
|
||||
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
|
||||
┃ Module Name ┃
|
||||
┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
|
||||
│ bandage/image │
|
||||
│ bcftools/consensus │
|
||||
│ bcftools/filter │
|
||||
│ bcftools/isec │
|
||||
..truncated..
|
||||
```
|
||||
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
|
||||
┃ Module Name ┃
|
||||
┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
|
||||
│ bandage/image │
|
||||
│ bcftools/consensus │
|
||||
│ bcftools/filter │
|
||||
│ bcftools/isec │
|
||||
..truncated..
|
||||
```
|
||||
|
||||
3. Install the module in your pipeline directory:
|
||||
|
||||
```console
|
||||
$ nf-core modules install fastqc
|
||||
```console
|
||||
$ nf-core modules install fastqc
|
||||
|
||||
,--./,-.
|
||||
___ __ __ __ ___ /,-._.--~\
|
||||
|\ | |__ __ / ` / \ |__) |__ } {
|
||||
| \| | \__, \__/ | \ |___ \`-._,-`-,
|
||||
`._,._,'
|
||||
,--./,-.
|
||||
___ __ __ __ ___ /,-._.--~\
|
||||
|\ | |__ __ / ` / \ |__) |__ } {
|
||||
| \| | \__, \__/ | \ |___ \`-._,-`-,
|
||||
`._,._,'
|
||||
|
||||
nf-core/tools version 2.0
|
||||
nf-core/tools version 2.0
|
||||
|
||||
INFO Installing fastqc pipeline_modules.py:213
|
||||
INFO Downloaded 3 files to ./modules/nf-core/modules/fastqc pipeline_modules.py:236
|
||||
```
|
||||
INFO Installing fastqc pipeline_modules.py:213
|
||||
INFO Downloaded 3 files to ./modules/nf-core/modules/fastqc pipeline_modules.py:236
|
||||
```
|
||||
|
||||
4. Import the module in your Nextflow script:
|
||||
|
||||
```nextflow
|
||||
#!/usr/bin/env nextflow
|
||||
```nextflow
|
||||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { FASTQC } from './modules/nf-core/modules/fastqc/main'
|
||||
```
|
||||
include { FASTQC } from './modules/nf-core/modules/fastqc/main'
|
||||
```
|
||||
|
||||
5. Remove the module from the pipeline repository if required:
|
||||
|
||||
```console
|
||||
$ nf-core modules remove fastqc
|
||||
```console
|
||||
$ nf-core modules remove fastqc
|
||||
|
||||
,--./,-.
|
||||
___ __ __ __ ___ /,-._.--~\
|
||||
|\ | |__ __ / ` / \ |__) |__ } {
|
||||
| \| | \__, \__/ | \ |___ \`-._,-`-,
|
||||
`._,._,'
|
||||
,--./,-.
|
||||
___ __ __ __ ___ /,-._.--~\
|
||||
|\ | |__ __ / ` / \ |__) |__ } {
|
||||
| \| | \__, \__/ | \ |___ \`-._,-`-,
|
||||
`._,._,'
|
||||
|
||||
nf-core/tools version 2.0
|
||||
nf-core/tools version 2.0
|
||||
|
||||
INFO Removing fastqc pipeline_modules.py:271
|
||||
INFO Successfully removed fastqc pipeline_modules.py:285
|
||||
```
|
||||
INFO Removing fastqc pipeline_modules.py:271
|
||||
INFO Successfully removed fastqc pipeline_modules.py:285
|
||||
```
|
||||
|
||||
6. Check that a locally installed nf-core module is up-to-date compared to the one hosted in this repo:
|
||||
|
||||
```console
|
||||
$ nf-core modules lint fastqc
|
||||
```console
|
||||
$ nf-core modules lint fastqc
|
||||
|
||||
,--./,-.
|
||||
___ __ __ __ ___ /,-._.--~\
|
||||
|\ | |__ __ / ` / \ |__) |__ } {
|
||||
| \| | \__, \__/ | \ |___ \`-._,-`-,
|
||||
`._,._,'
|
||||
,--./,-.
|
||||
___ __ __ __ ___ /,-._.--~\
|
||||
|\ | |__ __ / ` / \ |__) |__ } {
|
||||
| \| | \__, \__/ | \ |___ \`-._,-`-,
|
||||
`._,._,'
|
||||
|
||||
nf-core/tools version 2.0
|
||||
nf-core/tools version 2.0
|
||||
|
||||
INFO Linting pipeline: . lint.py:104
|
||||
INFO Linting module: fastqc lint.py:106
|
||||
INFO Linting pipeline: . lint.py:104
|
||||
INFO Linting module: fastqc lint.py:106
|
||||
|
||||
╭─────────────────────────────────────────────────────────────────────────────────╮
|
||||
│ [!] 1 Test Warning │
|
||||
╰─────────────────────────────────────────────────────────────────────────────────╯
|
||||
╭──────────────┬───────────────────────────────┬──────────────────────────────────╮
|
||||
│ Module name │ Test message │ File path │
|
||||
├──────────────┼───────────────────────────────┼──────────────────────────────────┤
|
||||
│ fastqc │ Local copy of module outdated │ modules/nf-core/modules/fastqc/ │
|
||||
╰──────────────┴────────────────────────────── ┴──────────────────────────────────╯
|
||||
╭──────────────────────╮
|
||||
│ LINT RESULTS SUMMARY │
|
||||
├──────────────────────┤
|
||||
│ [✔] 15 Tests Passed │
|
||||
│ [!] 1 Test Warning │
|
||||
│ [✗] 0 Test Failed │
|
||||
╰──────────────────────╯
|
||||
```
|
||||
╭─────────────────────────────────────────────────────────────────────────────────╮
|
||||
│ [!] 1 Test Warning │
|
||||
╰─────────────────────────────────────────────────────────────────────────────────╯
|
||||
╭──────────────┬───────────────────────────────┬──────────────────────────────────╮
|
||||
│ Module name │ Test message │ File path │
|
||||
├──────────────┼───────────────────────────────┼──────────────────────────────────┤
|
||||
│ fastqc │ Local copy of module outdated │ modules/nf-core/modules/fastqc/ │
|
||||
╰──────────────┴────────────────────────────── ┴──────────────────────────────────╯
|
||||
╭──────────────────────╮
|
||||
│ LINT RESULTS SUMMARY │
|
||||
├──────────────────────┤
|
||||
│ [✔] 15 Tests Passed │
|
||||
│ [!] 1 Test Warning │
|
||||
│ [✗] 0 Test Failed │
|
||||
╰──────────────────────╯
|
||||
```
|
||||
|
||||
## 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 :)
|
||||
|
||||
|
|
|
|||
|
|
@ -15,6 +15,9 @@ process ABACAS {
|
|||
tuple val(meta), path('*.abacas*'), emit: results
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -14,7 +14,7 @@ tools:
|
|||
documentation: http://abacas.sourceforge.net/documentation.html
|
||||
tool_dev_url: None
|
||||
doi: "10.1093/bioinformatics/btp347"
|
||||
licence: ['GPL v2-or-later']
|
||||
licence: ["GPL v2-or-later"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
34
modules/abricate/run/main.nf
Normal file
34
modules/abricate/run/main.nf
Normal file
|
|
@ -0,0 +1,34 @@
|
|||
process ABRICATE_RUN {
|
||||
tag "$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
43
modules/abricate/run/meta.yml
Normal file
|
|
@ -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
33
modules/abricate/summary/main.nf
Normal file
|
|
@ -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
43
modules/abricate/summary/meta.yml
Normal file
|
|
@ -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"
|
||||
|
|
@ -9,46 +9,46 @@ 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
|
||||
path "versions.yml" , emit: versions
|
||||
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:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
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}":
|
||||
|
|
@ -60,15 +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")
|
||||
|
|
|
|||
|
|
@ -1,50 +1,90 @@
|
|||
name: adapterremoval
|
||||
description: Trim sequencing adapters and collapse overlapping reads
|
||||
keywords:
|
||||
- trimming
|
||||
- adapters
|
||||
- merging
|
||||
- fastq
|
||||
- trimming
|
||||
- adapters
|
||||
- merging
|
||||
- fastq
|
||||
tools:
|
||||
- adapterremoval:
|
||||
description: The AdapterRemoval v2 tool for merging and clipping reads.
|
||||
homepage: https://github.com/MikkelSchubert/adapterremoval
|
||||
documentation: https://adapterremoval.readthedocs.io
|
||||
licence: ['GPL v3']
|
||||
- adapterremoval:
|
||||
description: The AdapterRemoval v2 tool for merging and clipping reads.
|
||||
homepage: https://github.com/MikkelSchubert/adapterremoval
|
||||
documentation: https://adapterremoval.readthedocs.io
|
||||
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}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
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 ]
|
||||
- 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}"
|
||||
- log:
|
||||
type: file
|
||||
description: AdapterRemoval log file
|
||||
pattern: "*.log"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- 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: "*.settings"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
|
||||
authors:
|
||||
- "@maxibor"
|
||||
- "@maxibor"
|
||||
- "@jfy133"
|
||||
|
|
|
|||
38
modules/adapterremovalfixprefix/main.nf
Normal file
38
modules/adapterremovalfixprefix/main.nf
Normal file
|
|
@ -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: $VERSION
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
43
modules/adapterremovalfixprefix/meta.yml
Normal file
43
modules/adapterremovalfixprefix/meta.yml
Normal file
|
|
@ -0,0 +1,43 @@
|
|||
name: adapterremovalfixprefix
|
||||
description: Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.
|
||||
keywords:
|
||||
- adapterremoval
|
||||
- fastq
|
||||
- dedup
|
||||
tools:
|
||||
- adapterremovalfixprefix:
|
||||
description: Fixes adapter removal prefixes to make sure no clashing read names are in the output.
|
||||
homepage: https://github.com/apeltzer/AdapterRemovalFixPrefix
|
||||
documentation: None
|
||||
tool_dev_url: https://github.com/apeltzer/AdapterRemovalFixPrefix
|
||||
doi: "10.1186/s13059-016-0918-z"
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fastq:
|
||||
type: file
|
||||
description: FASTQ file from AdapterRemoval2
|
||||
pattern: "*.{fq.gz,fastq.gz}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- fixed_fastq:
|
||||
type: file
|
||||
description: FASTQ file with fixed read prefixes for DeDup
|
||||
pattern: "*.{fq.gz}"
|
||||
|
||||
authors:
|
||||
- "@jfy133"
|
||||
|
|
@ -15,6 +15,9 @@ process AGRVATE {
|
|||
path "${fasta.baseName}-results" , emit: results_dir
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://github.com/VishnuRaghuram94/AgrVATE
|
||||
tool_dev_url: https://github.com/VishnuRaghuram94/AgrVATE
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -16,6 +16,9 @@ process ALLELECOUNTER {
|
|||
tuple val(meta), path("*.alleleCount"), emit: allelecount
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -32,8 +32,8 @@ input:
|
|||
description: loci file <CHR><tab><POS1>
|
||||
pattern: "*.{tsv}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file. Required when passing CRAM files.
|
||||
type: file
|
||||
description: Input genome fasta file. Required when passing CRAM files.
|
||||
|
||||
output:
|
||||
- meta:
|
||||
|
|
|
|||
41
modules/amplify/predict/main.nf
Normal file
41
modules/amplify/predict/main.nf
Normal file
|
|
@ -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
|
||||
"""
|
||||
}
|
||||
47
modules/amplify/predict/meta.yml
Normal file
47
modules/amplify/predict/meta.yml
Normal file
|
|
@ -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"
|
||||
|
|
@ -18,6 +18,9 @@ process AMPS {
|
|||
path "results/pdf_candidate_profiles/" , emit: candidate_pdfs
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -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
modules/amrfinderplus/run/main.nf
Normal file
55
modules/amrfinderplus/run/main.nf
Normal file
|
|
@ -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
modules/amrfinderplus/run/meta.yml
Normal file
51
modules/amrfinderplus/run/meta.yml
Normal file
|
|
@ -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
modules/amrfinderplus/update/main.nf
Normal file
29
modules/amrfinderplus/update/main.nf
Normal file
|
|
@ -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
modules/amrfinderplus/update/meta.yml
Normal file
37
modules/amrfinderplus/update/meta.yml
Normal file
|
|
@ -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"
|
||||
56
modules/antismash/antismashlitedownloaddatabases/main.nf
Normal file
56
modules/antismash/antismashlitedownloaddatabases/main.nf
Normal file
|
|
@ -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
|
||||
"""
|
||||
}
|
||||
60
modules/antismash/antismashlitedownloaddatabases/meta.yml
Normal file
60
modules/antismash/antismashlitedownloaddatabases/meta.yml
Normal file
|
|
@ -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"
|
||||
|
|
@ -2,25 +2,38 @@ 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
|
||||
tuple val(meta), path("*.fusions.discarded.tsv"), emit: fusions_fail
|
||||
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 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 \\
|
||||
|
|
@ -29,6 +42,10 @@ process ARRIBA {
|
|||
-o ${prefix}.fusions.tsv \\
|
||||
-O ${prefix}.fusions.discarded.tsv \\
|
||||
$blacklist \\
|
||||
$known_fusions \\
|
||||
$structural_variants \\
|
||||
$tags \\
|
||||
$protein_domains \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
|
|
@ -36,4 +53,14 @@ process ARRIBA {
|
|||
arriba: \$(arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
|
||||
stub:
|
||||
def prefix = task.ext.prefix ?: "${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
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
|
|
|||
|
|
@ -14,6 +14,9 @@ process ARTIC_GUPPYPLEX {
|
|||
tuple val(meta), path("*.fastq.gz"), emit: 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 ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://artic.readthedocs.io/en/latest/
|
||||
tool_dev_url: https://github.com/artic-network/fieldbioinformatics
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -13,7 +13,8 @@ process ARTIC_MINION {
|
|||
path sequencing_summary
|
||||
path ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta")
|
||||
path ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed")
|
||||
path medaka_model
|
||||
path medaka_model_file
|
||||
val medaka_model_string
|
||||
val scheme
|
||||
val scheme_version
|
||||
|
||||
|
|
@ -31,6 +32,9 @@ process ARTIC_MINION {
|
|||
tuple val(meta), path("*.json"), optional:true , emit: json
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
@ -41,7 +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"
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
name: artic_minion
|
||||
description: |
|
||||
Run the alignment/variant-call/consensus logic of the artic pipeline
|
||||
Run the alignment/variant-call/consensus logic of the artic pipeline
|
||||
keywords:
|
||||
- artic
|
||||
- aggregate
|
||||
|
|
@ -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
|
||||
|
|
@ -21,11 +21,11 @@ input:
|
|||
e.g. [ id:'test', single_end:false ]
|
||||
- fastq:
|
||||
type: file
|
||||
description: FastQ file containing reads
|
||||
description: FastQ file containing reads
|
||||
pattern: "*.{fastq.gz}"
|
||||
- fast5_dir:
|
||||
type: directory
|
||||
description: Directory containing MinION FAST5 files
|
||||
description: Directory containing MinION FAST5 files
|
||||
pattern: "*"
|
||||
- sequencing_summary:
|
||||
type: file
|
||||
|
|
@ -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
155
modules/ascat/main.nf
Normal 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
92
modules/ascat/meta.yml
Normal 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"
|
||||
|
|
@ -14,6 +14,9 @@ process ASSEMBLYSCAN {
|
|||
tuple val(meta), path("*.json"), emit: json
|
||||
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}"
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
|
|||
|
|
@ -19,6 +19,9 @@ process ATAQV_ATAQV {
|
|||
tuple val(meta), path("*.problems") , emit: problems, optional: true
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ tools:
|
|||
documentation: https://github.com/ParkerLab/ataqv/blob/master/README.rst
|
||||
tool_dev_url: https://github.com/ParkerLab/ataqv
|
||||
doi: "https://doi.org/10.1016/j.cels.2020.02.009"
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process BAKTA {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bakta:1.2.2--pyhdfd78af_0' :
|
||||
'quay.io/biocontainers/bakta:1.2.2--pyhdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/bakta:1.4.0--pyhdfd78af_1' :
|
||||
'quay.io/biocontainers/bakta:1.4.0--pyhdfd78af_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
|
@ -23,8 +23,12 @@ process BAKTA {
|
|||
tuple val(meta), path("${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("${prefix}.txt") , emit: txt
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
@ -58,6 +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}":
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
|
|
|||
|
|
@ -14,6 +14,9 @@ process BAMALIGNCLEANER {
|
|||
tuple val(meta), path("*.bam"), emit: bam
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@ tools:
|
|||
homepage: https://github.com/maxibor/bamAlignCleaner
|
||||
documentation: https://github.com/maxibor/bamAlignCleaner
|
||||
tool_dev_url: https://github.com/maxibor/bamAlignCleaner
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
38
modules/bamcmp/main.nf
Normal file
38
modules/bamcmp/main.nf
Normal file
|
|
@ -0,0 +1,38 @@
|
|||
def VERSION = '2.2'
|
||||
process BAMCMP {
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bamcmp=2.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bamcmp:2.2--h05f6578_0' :
|
||||
'quay.io/biocontainers/bamcmp:2.2--h05f6578_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(sample), path(contaminant)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*primary.bam") , emit: bam
|
||||
tuple val(meta), path("*contamination.bam"), emit: contamination_bam
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
bamcmp \\
|
||||
-1 $sample \\
|
||||
-2 $contaminant \\
|
||||
-A ${prefix}_primary.bam \\
|
||||
-B ${prefix}_contamination.bam \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
bamcmp: $VERSION
|
||||
END_VERSIONS
|
||||
"""
|
||||
|
||||
}
|
||||
58
modules/bamcmp/meta.yml
Normal file
58
modules/bamcmp/meta.yml
Normal file
|
|
@ -0,0 +1,58 @@
|
|||
name: bamcmp
|
||||
description: Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX).
|
||||
keywords:
|
||||
- filter
|
||||
- xenograft
|
||||
- host
|
||||
- graft
|
||||
- contamination
|
||||
- mouse
|
||||
|
||||
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,
|
||||
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"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test']
|
||||
|
||||
- sample:
|
||||
type: file
|
||||
description: BAM/CRAM/SAM file with the reads aligned to the primary genome (the one you want to keep)
|
||||
pattern: "*.{bam,cram,sam}"
|
||||
|
||||
- contaminant:
|
||||
type: file
|
||||
description: BAM/CRAM/SAM file with the reads aligned to the contaminant genome (the one you want to filter out)
|
||||
pattern: "*.{bam,cram,sam}"
|
||||
|
||||
output:
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
|
||||
- bam:
|
||||
type: file
|
||||
description: Bam file containing the reads which align better to the primary genome.
|
||||
pattern: "*.{bam,cram,sam}"
|
||||
|
||||
- bam:
|
||||
type: file
|
||||
description: Bam file containing the reads which align better to the contaminant genome.
|
||||
pattern: "*.{bam,cram,sam}"
|
||||
|
||||
authors:
|
||||
- "@kmurat1"
|
||||
- "@sppearce"
|
||||
41
modules/bamtools/convert/main.nf
Normal file
41
modules/bamtools/convert/main.nf
Normal file
|
|
@ -0,0 +1,41 @@
|
|||
process BAMTOOLS_CONVERT {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
|
||||
'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.{bed,fasta,fastq,json,pileup,sam,yaml}"), emit: data
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def test = args ==~ /-format (bed|fasta|fastq|json|pileup|sam|yaml)/
|
||||
if ( test == false ) error "-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml"
|
||||
m = args =~ /-format ([a-z]+)/
|
||||
ext = m[0][1]
|
||||
|
||||
|
||||
"""
|
||||
bamtools \\
|
||||
convert \\
|
||||
$args \\
|
||||
-in $bam \\
|
||||
-out ${prefix}.${ext}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
52
modules/bamtools/convert/meta.yml
Normal file
52
modules/bamtools/convert/meta.yml
Normal file
|
|
@ -0,0 +1,52 @@
|
|||
name: bamtools_convert
|
||||
description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
|
||||
keywords:
|
||||
- bamtools
|
||||
- bamtools/convert
|
||||
- bam
|
||||
- convert
|
||||
- bed
|
||||
- fasta
|
||||
- fastq
|
||||
- json
|
||||
- pileup
|
||||
- sam
|
||||
- yaml
|
||||
tools:
|
||||
- bamtools:
|
||||
description: C++ API & command-line toolkit for working with BAM data
|
||||
homepage: http://github.com/pezmaster31/bamtools
|
||||
documentation: https://github.com/pezmaster31/bamtools/wiki
|
||||
tool_dev_url: http://github.com/pezmaster31/bamtools
|
||||
doi: ""
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM file
|
||||
pattern: "*.bam"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
## TODO nf-core: Delete / customise this example output
|
||||
- out:
|
||||
type: file
|
||||
description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml)
|
||||
pattern: "*.{bed,fasta,fastq,json,pileup,sam,yaml}"
|
||||
|
||||
authors:
|
||||
- "@sguizard"
|
||||
|
|
@ -2,10 +2,10 @@ process BAMTOOLS_SPLIT {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
|
||||
'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
|
||||
'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0' :
|
||||
'quay.io/biocontainers/bamtools:2.5.2--hd03093a_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
@ -14,14 +14,21 @@ process BAMTOOLS_SPLIT {
|
|||
tuple val(meta), path("*.bam"), emit: bam
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def input_list = bam.collect{"-in $it"}.join(' ')
|
||||
"""
|
||||
bamtools \\
|
||||
split \\
|
||||
-in $bam \\
|
||||
$args
|
||||
merge \\
|
||||
$input_list \\
|
||||
| bamtools \\
|
||||
split \\
|
||||
-stub $prefix \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
|
|
|||
|
|
@ -14,6 +14,9 @@ process BAMUTIL_TRIMBAM {
|
|||
tuple val(meta), path("*.bam"), emit: bam
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ tools:
|
|||
documentation: https://genome.sph.umich.edu/wiki/BamUtil:_trimBam
|
||||
tool_dev_url: https://github.com/statgen/bamUtil
|
||||
doi: "10.1101/gr.176552.114"
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -15,6 +15,9 @@ process BANDAGE_IMAGE {
|
|||
tuple val(meta), path('*.svg'), emit: svg
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -1,44 +1,44 @@
|
|||
name: bandage_image
|
||||
description: Render an assembly graph in GFA 1.0 format to PNG and SVG image formats
|
||||
keywords:
|
||||
- gfa
|
||||
- graph
|
||||
- assembly
|
||||
- visualisation
|
||||
- gfa
|
||||
- graph
|
||||
- assembly
|
||||
- visualisation
|
||||
tools:
|
||||
- bandage:
|
||||
description: |
|
||||
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']
|
||||
- bandage:
|
||||
description: |
|
||||
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"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- gfa:
|
||||
type: file
|
||||
description: Assembly graph in GFA 1.0 format
|
||||
pattern: "*.gfa"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- gfa:
|
||||
type: file
|
||||
description: Assembly graph in GFA 1.0 format
|
||||
pattern: "*.gfa"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- png:
|
||||
type: file
|
||||
description: Bandage image in PNG format
|
||||
pattern: "*.png"
|
||||
- svg:
|
||||
type: file
|
||||
description: Bandage image in SVG format
|
||||
pattern: "*.svg"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- png:
|
||||
type: file
|
||||
description: Bandage image in PNG format
|
||||
pattern: "*.png"
|
||||
- svg:
|
||||
type: file
|
||||
description: Bandage image in SVG format
|
||||
pattern: "*.svg"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@heuermh"
|
||||
- "@heuermh"
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
@ -16,6 +16,9 @@ process BBMAP_ALIGN {
|
|||
tuple val(meta), path("*.log"), emit: log
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ tools:
|
|||
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
|
||||
tool_dev_url: None
|
||||
doi: ""
|
||||
licence: ['UC-LBL license (see package)']
|
||||
licence: ["UC-LBL license (see package)"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
@ -24,14 +24,14 @@ input:
|
|||
- fastq:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- ref:
|
||||
type: file
|
||||
description: |
|
||||
Either "ref" a directory containing an index, the name of another directory
|
||||
with a "ref" subdirectory containing an index or the name of a fasta formatted
|
||||
nucleotide file containg the reference to map to.
|
||||
Either "ref" a directory containing an index, the name of another directory
|
||||
with a "ref" subdirectory containing an index or the name of a fasta formatted
|
||||
nucleotide file containg the reference to map to.
|
||||
|
||||
output:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -16,6 +16,9 @@ process BBMAP_BBDUK {
|
|||
tuple val(meta), path('*.log') , emit: log
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
@ -20,14 +20,14 @@ input:
|
|||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- contaminants:
|
||||
type: file
|
||||
description: |
|
||||
Reference files containing adapter and/or contaminant sequences for sequence kmer matching
|
||||
type: file
|
||||
description: |
|
||||
Reference files containing adapter and/or contaminant sequences for sequence kmer matching
|
||||
|
||||
output:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -20,6 +20,9 @@ process BBMAP_BBSPLIT {
|
|||
tuple val(meta), path('*txt') , optional:true, emit: stats
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ tools:
|
|||
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
|
||||
tool_dev_url: None
|
||||
doi: ""
|
||||
licence: ['UC-LBL license (see package)']
|
||||
licence: ["UC-LBL license (see package)"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -14,6 +14,9 @@ process BBMAP_INDEX {
|
|||
path 'ref' , emit: index
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
|
||||
tool_dev_url: None
|
||||
doi: ""
|
||||
licence: ['UC-LBL license (see package)']
|
||||
licence: ["UC-LBL license (see package)"]
|
||||
|
||||
input:
|
||||
- fasta:
|
||||
|
|
|
|||
39
modules/bbmap/pileup/main.nf
Normal file
39
modules/bbmap/pileup/main.nf
Normal file
|
|
@ -0,0 +1,39 @@
|
|||
process BBMAP_PILEUP {
|
||||
tag "$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
47
modules/bbmap/pileup/meta.yml
Normal 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
42
modules/bcftools/annotate/main.nf
Normal 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
45
modules/bcftools/annotate/meta.yml
Normal file
|
|
@ -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"
|
||||
|
|
@ -14,6 +14,9 @@ process BCFTOOLS_CONCAT {
|
|||
tuple val(meta), path("*.gz"), emit: vcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -1,43 +1,43 @@
|
|||
name: bcftools_concat
|
||||
description: Concatenate VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- concat
|
||||
- bcftools
|
||||
- VCF
|
||||
- variant calling
|
||||
- concat
|
||||
- bcftools
|
||||
- VCF
|
||||
|
||||
tools:
|
||||
- concat:
|
||||
description: |
|
||||
Concatenate VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- concat:
|
||||
description: |
|
||||
Concatenate VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF concatenated output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF concatenated output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@abhi18av"
|
||||
|
|
|
|||
|
|
@ -14,6 +14,9 @@ process BCFTOOLS_CONSENSUS {
|
|||
tuple val(meta), path('*.fa'), emit: fasta
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -1,49 +1,49 @@
|
|||
name: bcftools_consensus
|
||||
description: Compresses VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- consensus
|
||||
- VCF
|
||||
- variant calling
|
||||
- consensus
|
||||
- VCF
|
||||
tools:
|
||||
- consensus:
|
||||
description: |
|
||||
Create consensus sequence by applying VCF variants to a reference fasta file.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- consensus:
|
||||
description: |
|
||||
Create consensus sequence by applying VCF variants to a reference fasta file.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF file
|
||||
pattern: "*.{vcf}"
|
||||
- tbi:
|
||||
type: file
|
||||
description: tabix index file
|
||||
pattern: "*.{tbi}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF file
|
||||
pattern: "*.{vcf}"
|
||||
- tbi:
|
||||
type: file
|
||||
description: tabix index file
|
||||
pattern: "*.{tbi}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference consensus file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference consensus file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -14,6 +14,9 @@ process BCFTOOLS_FILTER {
|
|||
tuple val(meta), path("*.gz"), emit: vcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -1,41 +1,41 @@
|
|||
name: bcftools_filter
|
||||
description: Filters VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- filtering
|
||||
- VCF
|
||||
- variant calling
|
||||
- filtering
|
||||
- VCF
|
||||
tools:
|
||||
- filter:
|
||||
description: |
|
||||
Apply fixed-threshold filters to VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- filter:
|
||||
description: |
|
||||
Apply fixed-threshold filters to VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF input file
|
||||
pattern: "*.{vcf}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF input file
|
||||
pattern: "*.{vcf}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF filtered output file
|
||||
pattern: "*.{vcf}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF filtered output file
|
||||
pattern: "*.{vcf}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -15,6 +15,9 @@ process BCFTOOLS_INDEX {
|
|||
tuple val(meta), path("*.tbi"), optional:true, emit: tbi
|
||||
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}"
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
|
|||
|
|
@ -14,6 +14,9 @@ process BCFTOOLS_ISEC {
|
|||
tuple val(meta), path("${prefix}"), emit: results
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -1,49 +1,49 @@
|
|||
name: bcftools_isec
|
||||
description: Apply set operations to VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- intersect
|
||||
- union
|
||||
- complement
|
||||
- VCF
|
||||
- variant calling
|
||||
- intersect
|
||||
- union
|
||||
- complement
|
||||
- VCF
|
||||
tools:
|
||||
- isec:
|
||||
description: |
|
||||
Computes intersections, unions and complements of VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- isec:
|
||||
description: |
|
||||
Computes intersections, unions and complements of VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- tbis:
|
||||
type: files
|
||||
description: |
|
||||
List containing the tbi index files corresponding to the vcfs input files
|
||||
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- tbis:
|
||||
type: files
|
||||
description: |
|
||||
List containing the tbi index files corresponding to the vcfs input files
|
||||
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- results:
|
||||
type: directory
|
||||
description: Folder containing the set operations results perform on the vcf files
|
||||
pattern: "${prefix}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- results:
|
||||
type: directory
|
||||
description: Folder containing the set operations results perform on the vcf files
|
||||
pattern: "${prefix}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -14,6 +14,9 @@ process BCFTOOLS_MERGE {
|
|||
tuple val(meta), path("*.gz"), emit: vcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -1,47 +1,47 @@
|
|||
name: bcftools_merge
|
||||
description: Merge VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- merge
|
||||
- VCF
|
||||
- variant calling
|
||||
- merge
|
||||
- VCF
|
||||
tools:
|
||||
- merge:
|
||||
description: |
|
||||
Merge VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- merge:
|
||||
description: |
|
||||
Merge VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- tbis:
|
||||
type: files
|
||||
description: |
|
||||
List containing the tbi index files corresponding to the vcfs input files
|
||||
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- tbis:
|
||||
type: files
|
||||
description: |
|
||||
List containing the tbi index files corresponding to the vcfs input files
|
||||
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF merged output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF merged output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -19,6 +19,9 @@ process BCFTOOLS_MPILEUP {
|
|||
tuple val(meta), path("*.mpileup") , emit: mpileup, optional: true
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def args2 = task.ext.args2 ?: ''
|
||||
|
|
|
|||
|
|
@ -1,57 +1,57 @@
|
|||
name: bcftools_mpileup
|
||||
description: Compresses VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- mpileup
|
||||
- VCF
|
||||
- variant calling
|
||||
- mpileup
|
||||
- VCF
|
||||
tools:
|
||||
- mpileup:
|
||||
description: |
|
||||
Generates genotype likelihoods at each genomic position with coverage.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- mpileup:
|
||||
description: |
|
||||
Generates genotype likelihoods at each genomic position with coverage.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Input BAM file
|
||||
pattern: "*.{bam}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- save_mpileup:
|
||||
type: boolean
|
||||
description: Save mpileup file generated by bcftools mpileup
|
||||
patter: "*.mpileup"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Input BAM file
|
||||
pattern: "*.{bam}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- save_mpileup:
|
||||
type: boolean
|
||||
description: Save mpileup file generated by bcftools mpileup
|
||||
patter: "*.mpileup"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF gzipped output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- tbi:
|
||||
type: file
|
||||
description: tabix index file
|
||||
pattern: "*.{tbi}"
|
||||
- stats:
|
||||
type: file
|
||||
description: Text output file containing stats
|
||||
pattern: "*{stats.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF gzipped output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- tbi:
|
||||
type: file
|
||||
description: tabix index file
|
||||
pattern: "*.{tbi}"
|
||||
- stats:
|
||||
type: file
|
||||
description: Text output file containing stats
|
||||
pattern: "*{stats.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -15,6 +15,9 @@ process BCFTOOLS_NORM {
|
|||
tuple val(meta), path("*.gz") , emit: vcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
@ -31,4 +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
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -6,41 +6,41 @@ keywords:
|
|||
- variant calling
|
||||
- VCF
|
||||
tools:
|
||||
- norm:
|
||||
description: |
|
||||
Normalize VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- norm:
|
||||
description: |
|
||||
Normalize VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: |
|
||||
The vcf file to be normalized
|
||||
e.g. 'file1.vcf'
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: |
|
||||
The vcf file to be normalized
|
||||
e.g. 'file1.vcf'
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF normalized output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF normalized output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@abhi18av"
|
||||
- "@abhi18av"
|
||||
|
|
|
|||
|
|
@ -8,30 +8,32 @@ process BCFTOOLS_QUERY {
|
|||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(index)
|
||||
path(regions)
|
||||
path(targets)
|
||||
path(samples)
|
||||
tuple val(meta), path(vcf), path(tbi)
|
||||
path regions
|
||||
path targets
|
||||
path samples
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.gz") , emit: vcf
|
||||
tuple val(meta), path("*.txt"), emit: txt
|
||||
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 regions_file = regions ? "--regions-file ${regions}" : ""
|
||||
def regions_file = regions ? "--regions-file ${regions}" : ""
|
||||
def targets_file = targets ? "--targets-file ${targets}" : ""
|
||||
def samples_file = samples ? "--samples-file ${samples}" : ""
|
||||
|
||||
"""
|
||||
bcftools query \\
|
||||
--output ${prefix}.vcf.gz \\
|
||||
${regions_file} \\
|
||||
${targets_file} \\
|
||||
${samples_file} \\
|
||||
--output ${prefix}.txt \\
|
||||
$regions_file \\
|
||||
$targets_file \\
|
||||
$samples_file \\
|
||||
$args \\
|
||||
${vcf}
|
||||
$vcf
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
|||
|
|
@ -6,57 +6,56 @@ keywords:
|
|||
- bcftools
|
||||
- VCF
|
||||
tools:
|
||||
- query:
|
||||
description: |
|
||||
Extracts fields from VCF or BCF files and outputs them in user-defined format.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- query:
|
||||
description: |
|
||||
Extracts fields from VCF or BCF files and outputs them in user-defined format.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: |
|
||||
The vcf file to be qeuried.
|
||||
e.g. 'file.vcf'
|
||||
- index:
|
||||
type: file
|
||||
description: |
|
||||
The tab index for the VCF file to be inspected.
|
||||
e.g. 'file.tbi'
|
||||
- regions:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file.
|
||||
e.g. 'file.vcf'
|
||||
- targets:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
|
||||
e.g. 'file.vcf'
|
||||
- samples:
|
||||
type: file
|
||||
description: |
|
||||
Optional, file of sample names to be included or excluded.
|
||||
e.g. 'file.tsv'
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: |
|
||||
The vcf file to be qeuried.
|
||||
pattern: "*.{vcf.gz, vcf}"
|
||||
- tbi:
|
||||
type: file
|
||||
description: |
|
||||
The tab index for the VCF file to be inspected.
|
||||
pattern: "*.tbi"
|
||||
- regions:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file.
|
||||
- targets:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
|
||||
- samples:
|
||||
type: file
|
||||
description: |
|
||||
Optional, file of sample names to be included or excluded.
|
||||
e.g. 'file.tsv'
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF query output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- txt:
|
||||
type: file
|
||||
description: BCFTools query output file
|
||||
pattern: "*.txt"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@abhi18av"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -16,6 +16,9 @@ process BCFTOOLS_REHEADER {
|
|||
tuple val(meta), path("*.vcf.gz"), emit: vcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ tools:
|
|||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://samtools.github.io/bcftools/bcftools.html#reheader
|
||||
doi: 10.1093/gigascience/giab008
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -14,6 +14,9 @@ process BCFTOOLS_SORT {
|
|||
tuple val(meta), path("*.gz"), emit: vcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
|
|
|||
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Reference in a new issue