nf-core · drpatelh · Feb 15, 2022 · Feb 7, 2022 · Feb 9, 2022 · Feb 9, 2022
@@ -12,9 +12,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: actions/setup-node@v1
-        with:
-          node-version: "10"
+      - uses: actions/setup-node@v2
 
       - name: Install markdownlint
         run: npm install -g markdownlint-cli
@@ -27,9 +25,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: actions/setup-node@v1
-        with:
-          node-version: "10"
+      - uses: actions/setup-node@v2
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -44,9 +40,7 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install NodeJS
-        uses: actions/setup-node@v1
-        with:
-          node-version: "10"
+        uses: actions/setup-node@v2
 
       - name: Install yaml-lint
         run: npm install -g yaml-lint

@@ -1,14 +1,14 @@
 image: nfcore/gitpod:latest
 
 vscode:
-  extensions: # based on nf-core.nf-core-extensionpack
+  extensions:  # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore                 # Language support for .gitignore files
-    # - cssho.vscode-svgviewer                 # SVG viewer
+    # - 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
-    # - nextflow.nextflow                      # Nextflow syntax highlighting
+    # - nextflow.nextflow                    # Nextflow syntax highlighting
     - oderwat.indent-rainbow                 # Highlight indentation level
     - streetsidesoftware.code-spell-checker  # Spelling checker for source code
@@ -8,4 +8,4 @@ header-increment: false
 no-duplicate-header:
     siblings_only: true
 ul-indent:
-  indent: 4
+    indent: 4
@@ -0,0 +1,5 @@
+extends: default
+
+rules:
+    document-start: disable
+    line-length: disable
diff --git a/modules/abacas/meta.yml b/modules/abacas/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: http://abacas.sourceforge.net/documentation.html
       tool_dev_url: None
       doi: "10.1093/bioinformatics/btp347"
-      licence: ['GPL v2-or-later']
+      licence: ["GPL v2-or-later"]
 
 input:
   - meta:

diff --git a/modules/adapterremoval/meta.yml b/modules/adapterremoval/meta.yml
@@ -1,50 +1,50 @@
 name: adapterremoval
 description: Trim sequencing adapters and collapse overlapping reads
 keywords:
-    - trimming
-    - adapters
-    - merging
-    - fastq
+  - trimming
+  - adapters
+  - merging
+  - fastq
 tools:
-    - adapterremoval:
-        description: The AdapterRemoval v2 tool for merging and clipping reads.
-        homepage: https://github.com/MikkelSchubert/adapterremoval
-        documentation: https://adapterremoval.readthedocs.io
-        licence: ['GPL v3']
+  - adapterremoval:
+      description: The AdapterRemoval v2 tool for merging and clipping reads.
+      homepage: https://github.com/MikkelSchubert/adapterremoval
+      documentation: https://adapterremoval.readthedocs.io
+      licence: ["GPL v3"]
 
 input:
-    - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false, collapse:false ]
-    - reads:
-        type: file
-        description: |
-          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-          respectively.
-        pattern: "*.{fq,fastq,fg.gz,fastq.gz}"
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false, collapse:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+      pattern: "*.{fq,fastq,fg.gz,fastq.gz}"
 
 output:
-    - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
-    - reads:
-        type: file
-        description: |
-          List of input adapter trimmed FastQ files of size 1 or 2 for
-          single-end or collapsed data and paired-end data, respectively.
-        pattern: "*.{fastq.gz}"
-    - log:
-        type: file
-        description: AdapterRemoval log file
-        pattern: "*.log"
-    - versions:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input adapter trimmed FastQ files of size 1 or 2 for
+        single-end or collapsed data and paired-end data, respectively.
+      pattern: "*.{fastq.gz}"
+  - log:
+      type: file
+      description: AdapterRemoval log file
+      pattern: "*.log"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
 
 authors:
-    - "@maxibor"
+  - "@maxibor"
diff --git a/modules/agrvate/meta.yml b/modules/agrvate/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: https://github.com/VishnuRaghuram94/AgrVATE
       tool_dev_url: https://github.com/VishnuRaghuram94/AgrVATE
       doi: ""
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

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

diff --git a/modules/arriba/meta.yml b/modules/arriba/meta.yml
@@ -10,7 +10,7 @@ tools:
       documentation: https://arriba.readthedocs.io/en/latest/
       tool_dev_url: https://github.com/suhrig/arriba
       doi: "10.1101/gr.257246.119"
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

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

diff --git a/modules/artic/minion/meta.yml b/modules/artic/minion/meta.yml
@@ -1,6 +1,6 @@
 name: artic_minion
 description: |
-    Run the alignment/variant-call/consensus logic of the artic pipeline
+  Run the alignment/variant-call/consensus logic of the artic pipeline
 keywords:
   - artic
   - aggregate
@@ -12,7 +12,7 @@ tools:
       documentation: https://artic.readthedocs.io/en/latest/
       tool_dev_url: https://github.com/artic-network/fieldbioinformatics
       doi: ""
-      licence: ['MIT']
+      licence: ["MIT"]
 input:
   - meta:
       type: map
@@ -21,11 +21,11 @@ input:
         e.g. [ id:'test', single_end:false ]
   - fastq:
       type: file
-      description:  FastQ file containing reads
+      description: FastQ file containing reads
       pattern: "*.{fastq.gz}"
   - fast5_dir:
       type: directory
-      description:  Directory containing MinION FAST5 files
+      description: Directory containing MinION FAST5 files
       pattern: "*"
   - sequencing_summary:
       type: file

diff --git a/modules/assemblyscan/meta.yml b/modules/assemblyscan/meta.yml
@@ -10,7 +10,7 @@ tools:
       documentation: https://github.com/rpetit3/assembly-scan
       tool_dev_url: https://github.com/rpetit3/assembly-scan
       doi: ""
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

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

diff --git a/modules/bakta/meta.yml b/modules/bakta/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: https://github.com/oschwengers/bakta
       tool_dev_url: https://github.com/oschwengers/bakta
       doi: "10.1099/mgen.0.000685"
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

diff --git a/modules/bamaligncleaner/meta.yml b/modules/bamaligncleaner/meta.yml
@@ -8,7 +8,7 @@ tools:
       homepage: https://github.com/maxibor/bamAlignCleaner
       documentation: https://github.com/maxibor/bamAlignCleaner
       tool_dev_url: https://github.com/maxibor/bamAlignCleaner
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:

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

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

diff --git a/modules/bamtools/split/meta.yml b/modules/bamtools/split/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: https://github.com/pezmaster31/bamtools/wiki
       tool_dev_url: http://github.com/pezmaster31/bamtools
       doi: ""
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:

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

diff --git a/modules/bandage/image/meta.yml b/modules/bandage/image/meta.yml
@@ -1,44 +1,44 @@
 name: bandage_image
 description: Render an assembly graph in GFA 1.0 format to PNG and SVG image formats
 keywords:
-    - gfa
-    - graph
-    - assembly
-    - visualisation
+  - gfa
+  - graph
+  - assembly
+  - visualisation
 tools:
-    - bandage:
-        description: |
-            Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
-        homepage: https://github.com/rrwick/Bandage
-        documentation: https://github.com/rrwick/Bandage
-        licence: ['GPL-3.0-or-later']
+  - bandage:
+    description: |
+      Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
+    homepage: https://github.com/rrwick/Bandage
+    documentation: https://github.com/rrwick/Bandage
+    licence: ["GPL-3.0-or-later"]
 input:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - gfa:
-        type: file
-        description: Assembly graph in GFA 1.0 format
-        pattern: "*.gfa"
+  - meta:
+    type: map
+    description: |
+      Groovy Map containing sample information
+      e.g. [ id:'test', single_end:false ]
+  - gfa:
+    type: file
+    description: Assembly graph in GFA 1.0 format
+    pattern: "*.gfa"
 output:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - png:
-        type: file
-        description: Bandage image in PNG format
-        pattern: "*.png"
-    - svg:
-        type: file
-        description: Bandage image in SVG format
-        pattern: "*.svg"
-    - versions:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+  - meta:
+    type: map
+    description: |
+      Groovy Map containing sample information
+      e.g. [ id:'test', single_end:false ]
+  - png:
+    type: file
+    description: Bandage image in PNG format
+    pattern: "*.png"
+  - svg:
+    type: file
+    description: Bandage image in SVG format
+    pattern: "*.svg"
+  - versions:
+    type: file
+    description: File containing software versions
+    pattern: "versions.yml"
 authors:
-    - "@heuermh"
+  - "@heuermh"