mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-21 10:48:18 +00:00
Prettier (#1405)
* style: Add prettier config files * build: Add prettier vscode extension * ci: Replace markdownlint and yamllint with prettier * style: Run prettier * style: Use indent of 2 for markdown as well https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358 * style: Fix indent * style: Let editorconfig take over tab widths * style: yaml => yml * ci: Run prettier once Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se> Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
This commit is contained in:
parent
979e57b7ac
commit
f080015754
69 changed files with 207 additions and 244 deletions
|
@ -8,5 +8,5 @@ trim_trailing_whitespace = true
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indent_size = 4
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indent_style = space
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[*.{yml,yaml}]
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[*.{md,yml,yaml}]
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indent_size = 2
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|
|
5
.github/CONTRIBUTING.md
vendored
5
.github/CONTRIBUTING.md
vendored
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@ -16,7 +16,9 @@ Contributions to the code are even more welcome ;)
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If you'd like to write some code for nf-core/modules, the standard workflow is as follows:
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|
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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
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* If there isn't one already, please create one so that others know you're working on this
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|
||||
- If there isn't one already, please create one so that others know you're working on this
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|
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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
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3. When adding a module file, follow the [guidelines](https://github.com/nf-core/modules#adding-a-new-module-file)
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4. Ensure that [tests are working locally](https://github.com/nf-core/modules#running-tests-locally)
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@ -40,7 +42,6 @@ These tests are run both with the latest available version of `Nextflow` and als
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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)).
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### Images and figures
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For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
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|
|
32
.github/workflows/code-linting.yml
vendored
32
.github/workflows/code-linting.yml
vendored
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@ -5,20 +5,21 @@ on:
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pull_request:
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branches: [master]
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|
||||
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||||
jobs:
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Markdown:
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Prettier:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Check out repository
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uses: actions/checkout@v2
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- uses: actions/setup-node@v2
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- name: Install NodeJS
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uses: actions/setup-node@v2
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- name: Install markdownlint
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run: npm install -g markdownlint-cli
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- name: Install Prettier
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run: npm install -g prettier
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- name: Run Markdownlint
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run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.markdownlint.yml
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- name: Run Prettier --check
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run: prettier --check .
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EditorConfig:
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runs-on: ubuntu-latest
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@ -32,18 +33,3 @@ jobs:
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- name: Run ECLint check
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run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
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YAML:
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runs-on: ubuntu-latest
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steps:
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- name: Check out repository
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uses: actions/checkout@v2
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- name: Install NodeJS
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uses: actions/setup-node@v2
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- name: Install yaml-lint
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run: npm install -g yaml-lint
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- name: Run yaml-lint
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run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yaml" -or -name "*.yml")
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|
|
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@ -4,7 +4,7 @@ vscode:
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extensions: # based on nf-core.nf-core-extensionpack
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- codezombiech.gitignore # Language support for .gitignore files
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# - cssho.vscode-svgviewer # SVG viewer
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- davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code
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- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
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- eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
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- EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
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- Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
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|
|
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@ -1,11 +0,0 @@
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# Markdownlint configuration file
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default: true
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line-length: false
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no-multiple-blanks: 0
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blanks-around-headers: false
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blanks-around-lists: false
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header-increment: false
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||||
no-duplicate-header:
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siblings_only: true
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ul-indent:
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indent: 4
|
16
.prettierignore
Normal file
16
.prettierignore
Normal file
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@ -0,0 +1,16 @@
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|||
includes/Maven_Pro/
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|
||||
# gitignore
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||||
.nextflow*
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work/
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results/
|
||||
test_output/
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||||
output/
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||||
.DS_Store
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*.code-workspace
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tests/data/
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.screenrc
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||||
.*.sw?
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__pycache__
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||||
*.pyo
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*.pyc
|
1
.prettierrc.yml
Normal file
1
.prettierrc.yml
Normal file
|
@ -0,0 +1 @@
|
|||
printWidth: 120
|
|
@ -1,5 +0,0 @@
|
|||
extends: default
|
||||
|
||||
rules:
|
||||
document-start: disable
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line-length: disable
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://github.com/tseemann/abricate
|
||||
tool_dev_url: https://github.com/tseemann/abricate
|
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doi: ""
|
||||
licence: ['GPL v2', 'GPL v2']
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||||
licence: ["GPL v2", "GPL v2"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://github.com/tseemann/abricate
|
||||
tool_dev_url: https://github.com/tseemann/abricate
|
||||
doi: ""
|
||||
licence: ['GPL v2', 'GPL v2']
|
||||
licence: ["GPL v2", "GPL v2"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -26,8 +26,7 @@ input:
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|||
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
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||||
- adapterlist:
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||||
type: file
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||||
description:
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||||
Optional text file containing list of adapters to look for for removal
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||||
description: Optional text file containing list of adapters to look for for removal
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||||
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.
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||||
|
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://github.com/ncbi/amr/wiki
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||||
tool_dev_url: https://github.com/ncbi/amr
|
||||
doi: "10.1038/s41598-021-91456-0"
|
||||
licence: ['Public Domain']
|
||||
licence: ["Public Domain"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://github.com/ncbi/amr/wiki
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||||
tool_dev_url: https://github.com/ncbi/amr
|
||||
doi: "10.1038/s41598-021-91456-0"
|
||||
licence: ['Public Domain']
|
||||
licence: ["Public Domain"]
|
||||
|
||||
input:
|
||||
- input_not_required:
|
||||
|
|
|
@ -9,7 +9,7 @@ tools:
|
|||
documentation: None
|
||||
tool_dev_url: https://github.com/Crick-CancerGenomics/ascat
|
||||
doi: "10.1093/bioinformatics/btaa538"
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- args:
|
||||
|
|
|
@ -12,7 +12,7 @@ tools:
|
|||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: https://samtools.github.io/bcftools/bcftools.html#annotate
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -2,8 +2,7 @@
|
|||
|
||||
Cell Ranger is a commercial tool from 10X Genomics. The container provided for the cellranger nf-core module is not provided nor supported by 10x Genomics. Updating the Cell Ranger versions in the container and pushing the update to Dockerhub needs to be done manually.
|
||||
|
||||
1. Navigate to the appropriate download page.
|
||||
- [Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest): download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
|
||||
1. Navigate to the appropriate download page. - [Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest): download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
|
||||
|
||||
2. Edit the Dockerfile. Update the Cell Ranger versions in this line:
|
||||
|
||||
|
|
|
@ -2,9 +2,7 @@
|
|||
|
||||
Bcl2fastq2 and Cell Ranger are commercial tools from Illumina and 10X Genomics, respectively. The container provided for the cellranger nf-core module is not provided nor supported by either Illumina or 10x Genomics. Updating the bcl2fastq2 or Cell Ranger versions in the container and pushing the update to Dockerhub needs to be done manually.
|
||||
|
||||
1. Navigate to the appropriate download pages.
|
||||
- [bcl2fastq2](https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html): download the linux rpm installer of the desired bcl2fastq2 version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
|
||||
- [Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest): download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
|
||||
1. Navigate to the appropriate download pages. - [bcl2fastq2](https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html): download the linux rpm installer of the desired bcl2fastq2 version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies. - [Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest): download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
|
||||
|
||||
2. Edit the Dockerfile. Update the bcl2fastq2 and Cell Ranger versions in this line:
|
||||
|
||||
|
|
|
@ -8,7 +8,7 @@ tools:
|
|||
documentation: https://github.com/abyzovlab/CNVpytor
|
||||
tool_dev_url: https://github.com/abyzovlab/CNVpytor
|
||||
doi: "10.1101/2021.01.27.428472v1"
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
|
@ -35,6 +35,5 @@ output:
|
|||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
|
||||
|
||||
authors:
|
||||
- "@sima-r"
|
||||
|
|
|
@ -10,7 +10,7 @@ tools:
|
|||
documentation: https://github.com/abyzovlab/CNVpytor
|
||||
tool_dev_url: https://github.com/abyzovlab/CNVpytor
|
||||
doi: "10.1101/2021.01.27.428472v1"
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -10,7 +10,7 @@ tools:
|
|||
documentation: https://github.com/abyzovlab/CNVpytor
|
||||
tool_dev_url: https://github.com/abyzovlab/CNVpytor
|
||||
doi: "10.1101/2021.01.27.428472v1"
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
@ -35,7 +35,6 @@ input:
|
|||
description: Index of reference fasta file
|
||||
pattern: "*.fai"
|
||||
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
|
@ -10,7 +10,7 @@ tools:
|
|||
documentation: https://github.com/abyzovlab/CNVpytor
|
||||
tool_dev_url: https://github.com/abyzovlab/CNVpytor
|
||||
doi: "10.1101/2021.01.27.428472v1"
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -13,7 +13,7 @@ tools:
|
|||
documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
|
||||
tool_dev_url: https://github.com/BoevaLab/FREEC/
|
||||
doi: "10.1093/bioinformatics/btq635"
|
||||
licence: ['GPL >=2']
|
||||
licence: ["GPL >=2"]
|
||||
|
||||
input:
|
||||
- args:
|
||||
|
@ -131,7 +131,6 @@ input:
|
|||
description: Sorted bed file containing capture regions (optional)
|
||||
pattern: "*.bed"
|
||||
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
|
@ -6,8 +6,7 @@ keywords:
|
|||
- tsv
|
||||
tools:
|
||||
- csvtk:
|
||||
description:
|
||||
CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit
|
||||
description: CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit
|
||||
that allows rapid data investigation and manipulation.
|
||||
homepage: https://bioinf.shenwei.me/csvtk/
|
||||
documentation: https://bioinf.shenwei.me/csvtk/
|
||||
|
|
|
@ -9,7 +9,7 @@ tools:
|
|||
documentation: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
|
||||
tool_dev_url: https://github.com/deeptools/deepTools/
|
||||
doi: "https://doi.org/10.1093/nar/gkw257"
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -13,7 +13,7 @@ tools:
|
|||
documentation: https://github.com/LANL-Bioinformatics/FaQCs
|
||||
tool_dev_url: https://github.com/LANL-Bioinformatics/FaQCs
|
||||
doi: "https://doi.org/10.1186/s12859-014-0366-2"
|
||||
licence: ['GPLv3 License']
|
||||
licence: ["GPLv3 License"]
|
||||
|
||||
## TODO nf-core: Add a description of all of the variables used as input
|
||||
input:
|
||||
|
|
|
@ -8,14 +8,15 @@ keywords:
|
|||
- Short_Variant_Discovery
|
||||
tools:
|
||||
- gatk4:
|
||||
description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
|
||||
description:
|
||||
Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
|
||||
with a primary focus on variant discovery and genotyping. Its powerful processing engine
|
||||
and high-performance computing features make it capable of taking on projects of any size.
|
||||
homepage: https://gatk.broadinstitute.org/hc/en-us
|
||||
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs
|
||||
tool_dev_url: https://github.com/broadinstitute/gatk
|
||||
doi: 10.1158/1538-7445.AM2017-3590
|
||||
licence: ['Apache-2.0']
|
||||
licence: ["Apache-2.0"]
|
||||
|
||||
input:
|
||||
- fasta:
|
||||
|
|
|
@ -24,8 +24,7 @@ input:
|
|||
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,
|
||||
description: List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
pattern: "*.fastq.gz"
|
||||
|
||||
|
|
|
@ -9,7 +9,7 @@ tools:
|
|||
documentation: https://gatk.broadinstitute.org/hc/en-us
|
||||
tool_dev_url: https://github.com/broadinstitute/gatk
|
||||
doi: "10.1158/1538-7445.AM2017-3590"
|
||||
licence: ['BSD-3-clause']
|
||||
licence: ["BSD-3-clause"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -56,7 +56,6 @@ input:
|
|||
description: Index file for the germline resource.
|
||||
pattern: "*.vcf.gz.tbi"
|
||||
|
||||
|
||||
output:
|
||||
- pileup:
|
||||
type: file
|
||||
|
|
|
@ -52,11 +52,11 @@ input:
|
|||
- resvcfs:
|
||||
type: list
|
||||
description: resource files to be used as truth, training and known sites resources, this imports the files into the module, file names are specified again in the resource_labels to be called via the command.
|
||||
pattern: '*/hapmap_3.3.hg38_chr21.vcf.gz'
|
||||
pattern: "*/hapmap_3.3.hg38_chr21.vcf.gz"
|
||||
- restbis:
|
||||
type: list
|
||||
description: tbis for the corresponding vcfs files to be used as truth, training and known resources.
|
||||
pattern: '*/hapmap_3.3.hg38_chr21.vcf.gz.tbi'
|
||||
pattern: "*/hapmap_3.3.hg38_chr21.vcf.gz.tbi"
|
||||
- reslabels:
|
||||
type: list
|
||||
description: labels for the resource files to be used as truth, training and known sites resources, label should include an identifier,which kind of resource(s) it is, prior value and name of the file.
|
||||
|
|
|
@ -12,7 +12,7 @@ tools:
|
|||
documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
|
||||
tool_dev_url: https://github.com/pha4ge/hAMRonization
|
||||
doi: ""
|
||||
licence: ['GNU Lesser General Public v3 (LGPL v3)']
|
||||
licence: ["GNU Lesser General Public v3 (LGPL v3)"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
|
||||
tool_dev_url: https://github.com/pha4ge/hAMRonization
|
||||
doi: ""
|
||||
licence: ['GNU Lesser General Public v3 (LGPL v3)']
|
||||
licence: ["GNU Lesser General Public v3 (LGPL v3)"]
|
||||
|
||||
input:
|
||||
- reports:
|
||||
|
|
|
@ -12,7 +12,7 @@ tools:
|
|||
documentation: http://hmmer.org/documentation.html
|
||||
tool_dev_url: https://github.com/EddyRivasLab/hmmer
|
||||
doi: "10.1371/journal.pcbi.1002195"
|
||||
licence: ['BSD']
|
||||
licence: ["BSD"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://github.com/jimmyliu1326/HpsuisSero
|
||||
tool_dev_url: https://github.com/jimmyliu1326/HpsuisSero
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -14,7 +14,7 @@ tools:
|
|||
documentation: https://github.com/broadinstitute/ichorCNA/wiki
|
||||
tool_dev_url: https://github.com/broadinstitute/ichorCNA
|
||||
doi: "10.1038/s41467-017-00965-y"
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- wigs:
|
||||
|
|
|
@ -13,7 +13,7 @@ tools:
|
|||
documentation: https://github.com/broadinstitute/ichorCNA/wiki
|
||||
tool_dev_url: https://github.com/broadinstitute/ichorCNA
|
||||
doi: "10.1038/s41467-017-00965-y"
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -10,7 +10,7 @@ tools:
|
|||
documentation: https://github.com/tseemann/legsta
|
||||
tool_dev_url: https://github.com/tseemann/legsta
|
||||
doi: ""
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -28,8 +28,7 @@ input:
|
|||
description: The control file
|
||||
- macs2_gsize:
|
||||
type: string
|
||||
description:
|
||||
Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9),
|
||||
description: Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9),
|
||||
'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8)
|
||||
|
||||
output:
|
||||
|
|
|
@ -10,7 +10,7 @@ tools:
|
|||
documentation: https://mafft.cbrc.jp/alignment/software/manual/manual.html
|
||||
tool_dev_url: https://mafft.cbrc.jp/alignment/software/source.html
|
||||
doi: "10.1093/nar/gkf436"
|
||||
licence: ['BSD']
|
||||
licence: ["BSD"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -10,7 +10,7 @@ tools:
|
|||
documentation: https://github.com/phac-nml/mob-suite
|
||||
tool_dev_url: https://github.com/phac-nml/mob-suite
|
||||
doi: "10.1099/mgen.0.000435"
|
||||
licence: ['Apache License, Version 2.0']
|
||||
licence: ["Apache License, Version 2.0"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -12,7 +12,7 @@ tools:
|
|||
documentation: https://github.com/xjtu-omics/msisensor-pro/wiki
|
||||
tool_dev_url: https://github.com/xjtu-omics/msisensor-pro
|
||||
doi: "doi.org/10.1016/j.gpb.2020.02.001"
|
||||
licence: ['Custom Licence']
|
||||
licence: ["Custom Licence"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://github.com/xjtu-omics/msisensor-pro/wiki
|
||||
tool_dev_url: https://github.com/xjtu-omics/msisensor-pro
|
||||
doi: "doi.org/10.1016/j.gpb.2020.02.001"
|
||||
licence: ['Custom Licence']
|
||||
licence: ["Custom Licence"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://github.com/parklab/NGSCheckMate
|
||||
tool_dev_url: https://github.com/parklab/NGSCheckMate
|
||||
doi: "doi:/10.1093/nar/gkx193"
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- files:
|
||||
|
|
|
@ -12,7 +12,7 @@ tools:
|
|||
homepage: https://broadinstitute.github.io/picard/
|
||||
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrReplaceReadGroups-Picard-
|
||||
tool_dev_url: https://github.com/broadinstitute/picard
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -11,7 +11,7 @@ tools:
|
|||
homepage: https://broadinstitute.github.io/picard/
|
||||
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036712531-CreateSequenceDictionary-Picard-
|
||||
tool_dev_url: https://github.com/broadinstitute/picard
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -10,7 +10,7 @@ tools:
|
|||
homepage: https://broadinstitute.github.io/picard/
|
||||
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036713471-FixMateInformation-Picard-
|
||||
tool_dev_url: https://github.com/broadinstitute/picard
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -8,7 +8,7 @@ tools:
|
|||
description: Java tools for working with NGS data in the BAM/CRAM/SAM and VCF format
|
||||
homepage: https://broadinstitute.github.io/picard/
|
||||
documentation: https://broadinstitute.github.io/picard/command-line-overview.html#SortVcf
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -12,7 +12,7 @@ tools:
|
|||
documentation: http://www.cog-genomics.org/plink/2.0/general_usage
|
||||
tool_dev_url: None
|
||||
doi: "10.1186/s13742-015-0047-8"
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://github.com/arpcard/rgi
|
||||
tool_dev_url: https://github.com/arpcard/rgi
|
||||
doi: "10.1093/nar/gkz935"
|
||||
licence: ['https://card.mcmaster.ca/about']
|
||||
licence: ["https://card.mcmaster.ca/about"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -11,7 +11,7 @@ tools:
|
|||
homepage: https://github.com/deweylab/RSEM
|
||||
documentation: https://github.com/deweylab/RSEM
|
||||
doi: https://doi.org/10.1186/1471-2105-12-323
|
||||
licence: ['GPL-3.0-or-later']
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
|
@ -10,7 +10,7 @@ tools:
|
|||
documentation: https://bioinf.shenwei.me/seqkit/usage/
|
||||
tool_dev_url: https://github.com/shenwei356/seqkit/
|
||||
doi: "10.1371/journal.pone.0163962"
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -8,7 +8,7 @@ tools:
|
|||
homepage: https://github.com/lh3/seqtk
|
||||
documentation: https://docs.csc.fi/apps/seqtk/
|
||||
tool_dev_url: https://github.com/lh3/seqtk
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -8,7 +8,7 @@ tools:
|
|||
homepage: https://github.com/lh3/seqtk
|
||||
documentation: https://docs.csc.fi/apps/seqtk/
|
||||
tool_dev_url: https://github.com/lh3/seqtk
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://github.com/phac-nml/sistr_cmd
|
||||
tool_dev_url: https://github.com/phac-nml/sistr_cmd
|
||||
doi: "10.1371/journal.pone.0147101"
|
||||
licence: ['Apache-2.0']
|
||||
licence: ["Apache-2.0"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -10,7 +10,7 @@ tools:
|
|||
documentation: https://sourmash.readthedocs.io/
|
||||
tool_dev_url: https://github.com/dib-lab/sourmash
|
||||
doi: "10.1186/s13059-016-0997-x"
|
||||
licence: ['BSD-3-clause']
|
||||
licence: ["BSD-3-clause"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://github.com/jimmyliu1326/SsuisSero
|
||||
tool_dev_url: https://github.com/jimmyliu1326/SsuisSero
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -12,7 +12,7 @@ tools:
|
|||
documentation: https://github.com/moonso/stranger
|
||||
tool_dev_url: https://github.com/moonso/stranger
|
||||
doi: "10.5281/zenodo.4548873"
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -13,10 +13,7 @@ tools:
|
|||
documentation: https://github.com/seqan/seqan
|
||||
tool_dev_url: https://github.com/seqan/seqan
|
||||
doi: ""
|
||||
licence:
|
||||
[
|
||||
"https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE",
|
||||
]
|
||||
licence: ["https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE"]
|
||||
|
||||
input:
|
||||
- fasta:
|
||||
|
|
|
@ -11,10 +11,7 @@ tools:
|
|||
documentation: https://github.com/seqan/seqan
|
||||
tool_dev_url: https://github.com/seqan/seqan
|
||||
doi: ""
|
||||
licence:
|
||||
[
|
||||
"https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE",
|
||||
]
|
||||
licence: ["https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
@ -5,6 +5,6 @@
|
|||
- gatk4/combinegvcfs
|
||||
files:
|
||||
- path: output/gatk4/test.combined.g.vcf.gz
|
||||
contains: ['VCFv4.2']
|
||||
contains: ["VCFv4.2"]
|
||||
- path: output/gatk4/versions.yml
|
||||
md5sum: 49d9c467f84b6a99a4da3ef161af26bd
|
||||
|
|
|
@ -57,10 +57,7 @@
|
|||
- gatk4/genotypegvcfs
|
||||
files:
|
||||
- path: output/gatk4/test.genotyped.vcf.gz
|
||||
contains:
|
||||
[
|
||||
"AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.05;SOR=0.693",
|
||||
]
|
||||
contains: ["AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.05;SOR=0.693"]
|
||||
- path: output/gatk4/test.genotyped.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input
|
||||
|
@ -109,8 +106,5 @@
|
|||
- gatk4/genotypegvcfs
|
||||
files:
|
||||
- path: output/gatk4/test.genotyped.vcf.gz
|
||||
contains:
|
||||
[
|
||||
"AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.66;SOR=0.693",
|
||||
]
|
||||
contains: ["AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.66;SOR=0.693"]
|
||||
- path: output/gatk4/test.genotyped.vcf.gz.tbi
|
||||
|
|
|
@ -6,7 +6,7 @@
|
|||
files:
|
||||
- path: output/hmmer/test.txt.gz
|
||||
contains:
|
||||
- '[ok]'
|
||||
- "[ok]"
|
||||
- path: output/hmmer/versions.yml
|
||||
md5sum: ed0808c10abd205c6bd0fb01f45259bb
|
||||
|
||||
|
@ -20,12 +20,12 @@
|
|||
md5sum: d3121aa33455074c566fb7f8fdcda7b0
|
||||
- path: output/hmmer/test.domtbl.gz
|
||||
contains:
|
||||
- '# [ok]'
|
||||
- "# [ok]"
|
||||
- path: output/hmmer/test.tbl.gz
|
||||
contains:
|
||||
- '# [ok]'
|
||||
- "# [ok]"
|
||||
- path: output/hmmer/test.txt.gz
|
||||
contains:
|
||||
- '[ok]'
|
||||
- "[ok]"
|
||||
- path: output/hmmer/versions.yml
|
||||
md5sum: ebdcb08ae540e840f7b5c4c75a3a2993
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
- ichorcna
|
||||
files:
|
||||
- path: output/ichorcna/PoN_median.txt
|
||||
contains: ['seqnames']
|
||||
contains: ["seqnames"]
|
||||
- path: output/ichorcna/versions.yml
|
||||
md5sum: 59a2121301113cc013bfae65935e07f1
|
||||
|
||||
|
@ -16,6 +16,6 @@
|
|||
- ichorcna
|
||||
files:
|
||||
- path: output/ichorcna/PoN_median.txt
|
||||
contains: ['seqnames']
|
||||
contains: ["seqnames"]
|
||||
- path: output/ichorcna/versions.yml
|
||||
md5sum: 31a5fcc0075dbe747f7736efbdb99644
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
- ichorcna/run
|
||||
files:
|
||||
- path: output/ichorcna/test.cna.seg
|
||||
contains: ['Corrected_Copy_Number']
|
||||
contains: ["Corrected_Copy_Number"]
|
||||
- path: output/ichorcna/test.params.txt
|
||||
md5sum: e39a579cdcc9576679f06dc5c22605a7
|
||||
- path: output/ichorcna/versions.yml
|
||||
|
@ -18,7 +18,7 @@
|
|||
- ichorcna/run
|
||||
files:
|
||||
- path: output/ichorcna/test.cna.seg
|
||||
contains: ['Corrected_Copy_Number']
|
||||
contains: ["Corrected_Copy_Number"]
|
||||
- path: output/ichorcna/test.params.txt
|
||||
md5sum: 0b97e0269cd0b571f5a85890f6ddb181
|
||||
- path: output/ichorcna/versions.yml
|
||||
|
|
|
@ -5,6 +5,6 @@
|
|||
- picard
|
||||
files:
|
||||
- path: output/picard/test.dict
|
||||
contains: ['SN:MT192765.1']
|
||||
contains: ["SN:MT192765.1"]
|
||||
- path: output/picard/versions.yml
|
||||
md5sum: b3d8c7ea65b8a6d3237b153d13fe2014
|
||||
|
|
|
@ -26,10 +26,7 @@
|
|||
- path: output/roary/results/gene_presence_absence.Rtab
|
||||
contains: ["Gene"]
|
||||
- path: output/roary/results/gene_presence_absence.csv
|
||||
contains:
|
||||
[
|
||||
'"Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences"',
|
||||
]
|
||||
contains: ['"Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences"']
|
||||
- path: output/roary/results/number_of_conserved_genes.Rtab
|
||||
contains: ["279"]
|
||||
- path: output/roary/results/number_of_genes_in_pan_genome.Rtab
|
||||
|
|
Loading…
Reference in a new issue