* 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:
Edmund Miller 2022-03-18 08:27:50 -05:00 committed by GitHub
parent 979e57b7ac
commit f080015754
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
69 changed files with 207 additions and 244 deletions

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@ -8,5 +8,5 @@ trim_trailing_whitespace = true
indent_size = 4
indent_style = space
[*.{yml,yaml}]
[*.{md,yml,yaml}]
indent_size = 2

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

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@ -5,20 +5,21 @@ on:
pull_request:
branches: [master]
jobs:
Markdown:
Prettier:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Check out repository
uses: actions/checkout@v2
- uses: actions/setup-node@v2
- name: Install NodeJS
uses: actions/setup-node@v2
- name: Install markdownlint
run: npm install -g markdownlint-cli
- name: Install Prettier
run: npm install -g prettier
- name: Run Markdownlint
run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.markdownlint.yml
- name: Run Prettier --check
run: prettier --check .
EditorConfig:
runs-on: ubuntu-latest
@ -32,18 +33,3 @@ jobs:
- name: Run ECLint check
run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
YAML:
runs-on: ubuntu-latest
steps:
- name: Check out repository
uses: actions/checkout@v2
- name: Install NodeJS
uses: actions/setup-node@v2
- name: Install yaml-lint
run: npm install -g yaml-lint
- name: Run yaml-lint
run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yaml" -or -name "*.yml")

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

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

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

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

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@ -1,5 +0,0 @@
extends: default
rules:
document-start: disable
line-length: disable

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@ -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:

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@ -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:

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@ -26,8 +26,7 @@ input:
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
- adapterlist:
type: file
description:
Optional text file containing list of adapters to look for for removal
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.

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@ -11,7 +11,7 @@ tools:
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']
licence: ["Public Domain"]
input:
- meta:

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@ -11,7 +11,7 @@ tools:
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']
licence: ["Public Domain"]
input:
- input_not_required:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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"

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@ -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:

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@ -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

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@ -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:

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@ -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

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@ -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/

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@ -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:

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@ -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:

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@ -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:

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@ -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"

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@ -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:

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@ -56,7 +56,6 @@ input:
description: Index file for the germline resource.
pattern: "*.vcf.gz.tbi"
output:
- pileup:
type: file

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@ -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.

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

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@ -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:

View file

@ -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

View file

@ -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

View file

@ -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

View file

@ -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

View file

@ -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

View file

@ -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

View file

@ -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