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>
2024-11-13 05:13:09 +00:00 · 2022-03-18 08:27:50 -05:00 · 2022-03-18 08:27:50 -05:00 · f080015754
commit f080015754
parent 979e57b7ac
69 changed files with 207 additions and 244 deletions
--- a/.editorconfig
+++ b/.editorconfig
@ -8,5 +8,5 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space

-[*.{yml,yaml}]
+[*.{md,yml,yaml}]
 indent_size = 2
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@ -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).
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@ -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 --git-aware`
-    - [ ] `PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`
-    - [ ] `PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`
+  - [ ] `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`
--- a/.github/workflows/code-linting.yml
+++ b/.github/workflows/code-linting.yml
@ -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")
--- a/.gitpod.yml
+++ b/.gitpod.yml
@ -1,14 +1,14 @@
 image: nfcore/gitpod:latest

 vscode:
-  extensions:  # based on nf-core.nf-core-extensionpack
-    - codezombiech.gitignore                 # Language support for .gitignore files
+  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
-    - 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
+    - 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
+    - oderwat.indent-rainbow # Highlight indentation level
+    - streetsidesoftware.code-spell-checker # Spelling checker for source code
--- a/.markdownlint.yml
+++ b/.markdownlint.yml
@ -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
--- a/.prettierignore
+++ b/.prettierignore
@ -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
--- a/.prettierrc.yml
+++ b/.prettierrc.yml
@ -0,0 +1 @@
+printWidth: 120
--- a/.yamllint.yml
+++ b/.yamllint.yml
@ -1,5 +0,0 @@
-extends: default
-
-rules:
-    document-start: disable
-    line-length: disable
--- a/README.md
+++ b/README.md
@ -31,105 +31,105 @@ 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

--- a/modules/abricate/run/meta.yml
+++ b/modules/abricate/run/meta.yml
@ -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:
--- a/modules/abricate/summary/meta.yml
+++ b/modules/abricate/summary/meta.yml
@ -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:
--- a/modules/adapterremoval/meta.yml
+++ b/modules/adapterremoval/meta.yml
@ -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.
--- a/modules/amrfinderplus/run/meta.yml
+++ b/modules/amrfinderplus/run/meta.yml
@ -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:
--- a/modules/amrfinderplus/update/meta.yml
+++ b/modules/amrfinderplus/update/meta.yml
@ -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:
--- a/modules/ascat/meta.yml
+++ b/modules/ascat/meta.yml
@ -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:
--- a/modules/bcftools/annotate/meta.yml
+++ b/modules/bcftools/annotate/meta.yml
@ -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:
--- a/modules/biscuit/pileup/meta.yml
+++ b/modules/biscuit/pileup/meta.yml
@ -27,9 +27,9 @@ input:
  - normal_bams:
      type: file(s)
      description: |
-              BAM files to be analyzed. If no tumor_bam file is provided, any number of "normal" BAMs may be provided
-              ("normal" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a
-              tumor BAM file is provided, exactly one normal (germline) BAM must be provided.
+        BAM files to be analyzed. If no tumor_bam file is provided, any number of "normal" BAMs may be provided
+        ("normal" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a
+        tumor BAM file is provided, exactly one normal (germline) BAM must be provided.
      pattern: "*.{bam}"
  - normal_bais:
      type: file(s)
@ -38,9 +38,9 @@ input:
  - tumor_bam:
      type: file(s)
      description: |
-              Optional. If a tumor BAM file is provided, pileup will run in "somatic" mode and will annotate variants with
-              their somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a
-              tumor BAM file is provided, exactly one normal BAM must be provided.
+        Optional. If a tumor BAM file is provided, pileup will run in "somatic" mode and will annotate variants with
+        their somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a
+        tumor BAM file is provided, exactly one normal BAM must be provided.
      pattern: "*.{bam}"
  - tumor_bai:
      type: file(s)
--- a/modules/cellranger/README.md
+++ b/modules/cellranger/README.md
@ -2,23 +2,22 @@

 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:

-    ```bash
-    ENV CELLRANGER_VER=<VERSION>
-    ```
+   ```bash
+   ENV CELLRANGER_VER=<VERSION>
+   ```

 3. Create and test the container:

-    ```bash
-    docker build . -t nfcore/cellranger:<VERSION>
-    ```
+   ```bash
+   docker build . -t nfcore/cellranger:<VERSION>
+   ```

 4. Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.

-    ```bash
-    docker push nfcore/cellranger:<VERSION>
-    ```
+   ```bash
+   docker push nfcore/cellranger:<VERSION>
+   ```
--- a/modules/cellranger/mkfastq/README.md
+++ b/modules/cellranger/mkfastq/README.md
@ -2,25 +2,23 @@

 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:

-    ```bash
-    ENV BCL2FASTQ2_VER=<VERSION> \
-        CELLRANGER_VER=<VERSION>
-    ```
+   ```bash
+   ENV BCL2FASTQ2_VER=<VERSION> \
+       CELLRANGER_VER=<VERSION>
+   ```

 3. Create and test the container:

-    ```bash
-    docker build . -t nfcore/cellrangermkfastq:<CELLRANGER_VERSION>
-    ```
+   ```bash
+   docker build . -t nfcore/cellrangermkfastq:<CELLRANGER_VERSION>
+   ```

 4. Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.

-    ```bash
-    docker push nfcore/cellrangermkfastq:<CELLRANGER_VERSION>
-    ```
+   ```bash
+   docker push nfcore/cellrangermkfastq:<CELLRANGER_VERSION>
+   ```
--- a/modules/cnvpytor/callcnvs/meta.yml
+++ b/modules/cnvpytor/callcnvs/meta.yml
@ -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"
--- a/modules/cnvpytor/histogram/meta.yml
+++ b/modules/cnvpytor/histogram/meta.yml
@ -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:
--- a/modules/cnvpytor/importreaddepth/meta.yml
+++ b/modules/cnvpytor/importreaddepth/meta.yml
@ -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
--- a/modules/cnvpytor/partition/meta.yml
+++ b/modules/cnvpytor/partition/meta.yml
@ -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:
--- a/modules/controlfreec/meta.yml
+++ b/modules/controlfreec/meta.yml
@ -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
--- a/modules/csvtk/split/meta.yml
+++ b/modules/csvtk/split/meta.yml
@ -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/
--- a/modules/deeptools/bamcoverage/meta.yml
+++ b/modules/deeptools/bamcoverage/meta.yml
@ -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:
--- a/modules/faqcs/meta.yml
+++ b/modules/faqcs/meta.yml
@ -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:
--- a/modules/gatk4/combinegvcfs/meta.yml
+++ b/modules/gatk4/combinegvcfs/meta.yml
@ -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:
--- a/modules/gatk4/fastqtosam/meta.yml
+++ b/modules/gatk4/fastqtosam/meta.yml
@ -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"

--- a/modules/gatk4/gatherpileupsummaries/meta.yml
+++ b/modules/gatk4/gatherpileupsummaries/meta.yml
@ -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:
--- a/modules/gatk4/getpileupsummaries/meta.yml
+++ b/modules/gatk4/getpileupsummaries/meta.yml
@ -56,7 +56,6 @@ input:
      description: Index file for the germline resource.
      pattern: "*.vcf.gz.tbi"

-
 output:
  - pileup:
      type: file
--- a/modules/gatk4/variantrecalibrator/meta.yml
+++ b/modules/gatk4/variantrecalibrator/meta.yml
@ -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.
--- a/modules/hamronization/deeparg/meta.yml
+++ b/modules/hamronization/deeparg/meta.yml
@ -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:
--- a/modules/hamronization/summarize/meta.yml
+++ b/modules/hamronization/summarize/meta.yml
@ -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:
--- a/modules/hmmer/hmmsearch/meta.yml
+++ b/modules/hmmer/hmmsearch/meta.yml
@ -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:
--- a/modules/hpsuissero/meta.yml
+++ b/modules/hpsuissero/meta.yml
@ -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:
--- a/modules/ichorcna/createpon/meta.yml
+++ b/modules/ichorcna/createpon/meta.yml
@ -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:
--- a/modules/ichorcna/run/meta.yml
+++ b/modules/ichorcna/run/meta.yml
@ -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:
--- a/modules/legsta/meta.yml
+++ b/modules/legsta/meta.yml
@ -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:
--- a/modules/macs2/callpeak/meta.yml
+++ b/modules/macs2/callpeak/meta.yml
@ -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:
--- a/modules/mafft/meta.yml
+++ b/modules/mafft/meta.yml
@ -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:
--- a/modules/mobsuite/recon/meta.yml
+++ b/modules/mobsuite/recon/meta.yml
@ -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:
--- a/modules/msisensorpro/msi_somatic/meta.yml
+++ b/modules/msisensorpro/msi_somatic/meta.yml
@ -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:
--- a/modules/msisensorpro/scan/meta.yml
+++ b/modules/msisensorpro/scan/meta.yml
@ -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:
--- a/modules/ngscheckmate/ncm/meta.yml
+++ b/modules/ngscheckmate/ncm/meta.yml
@ -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:
--- a/modules/picard/addorreplacereadgroups/meta.yml
+++ b/modules/picard/addorreplacereadgroups/meta.yml
@ -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:
--- a/modules/picard/createsequencedictionary/meta.yml
+++ b/modules/picard/createsequencedictionary/meta.yml
@ -7,11 +7,11 @@ keywords:
 tools:
  - picard:
      description: |
-            Creates a sequence dictionary file (with ".dict" extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools. The output file contains a header but no SAMRecords, and the header contains only sequence records.
+        Creates a sequence dictionary file (with ".dict" extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools. The output file contains a header but no SAMRecords, and the header contains only sequence records.
      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:
--- a/modules/picard/fixmateinformation/meta.yml
+++ b/modules/picard/fixmateinformation/meta.yml
@ -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:
--- a/modules/picard/sortvcf/meta.yml
+++ b/modules/picard/sortvcf/meta.yml
@ -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:
--- a/modules/plink2/score/meta.yml
+++ b/modules/plink2/score/meta.yml
@ -6,13 +6,13 @@ keywords:
 tools:
  - plink2:
      description: |
-          Whole genome association analysis toolset, designed to perform a range
-          of basic, large-scale analyses in a computationally efficient manner
+        Whole genome association analysis toolset, designed to perform a range
+        of basic, large-scale analyses in a computationally efficient manner
      homepage: http://www.cog-genomics.org/plink/2.0/
      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:
--- a/modules/rgi/main/meta.yml
+++ b/modules/rgi/main/meta.yml
@ -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:
--- a/modules/rsem/calculateexpression/meta.yml
+++ b/modules/rsem/calculateexpression/meta.yml
@ -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
--- a/modules/seqkit/pair/meta.yml
+++ b/modules/seqkit/pair/meta.yml
@ -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:
--- a/modules/seqtk/rename/meta.yml
+++ b/modules/seqtk/rename/meta.yml
@ -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:
--- a/modules/seqtk/seq/meta.yml
+++ b/modules/seqtk/seq/meta.yml
@ -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:
--- a/modules/sistr/meta.yml
+++ b/modules/sistr/meta.yml
@ -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:
--- a/modules/sourmash/sketch/meta.yml
+++ b/modules/sourmash/sketch/meta.yml
@ -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:
--- a/modules/ssuissero/meta.yml
+++ b/modules/ssuissero/meta.yml
@ -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:
--- a/modules/stranger/meta.yml
+++ b/modules/stranger/meta.yml
@ -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:
--- a/modules/yara/index/meta.yml
+++ b/modules/yara/index/meta.yml
@ -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:
--- a/modules/yara/mapper/meta.yml
+++ b/modules/yara/mapper/meta.yml
@ -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:
--- a/tests/modules/gatk4/combinegvcfs/test.yml
+++ b/tests/modules/gatk4/combinegvcfs/test.yml
@ -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
--- a/tests/modules/gatk4/genotypegvcfs/test.yml
+++ b/tests/modules/gatk4/genotypegvcfs/test.yml
@ -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
--- a/tests/modules/hmmer/hmmsearch/test.yml
+++ b/tests/modules/hmmer/hmmsearch/test.yml
@ -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
--- a/tests/modules/ichorcna/createpon/test.yml
+++ b/tests/modules/ichorcna/createpon/test.yml
@ -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
--- a/tests/modules/ichorcna/run/test.yml
+++ b/tests/modules/ichorcna/run/test.yml
@ -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
--- a/tests/modules/picard/createsequencedictionary/test.yml
+++ b/tests/modules/picard/createsequencedictionary/test.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
--- a/tests/modules/roary/test.yml
+++ b/tests/modules/roary/test.yml
@ -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