fix yaml files

.github/workflows/code-linting.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: actions/setup-node@v1
+      - uses: actions/setup-node@v2
         with:
           node-version: "10"
 
@@ -27,7 +27,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: actions/setup-node@v1
+      - uses: actions/setup-node@v2
         with:
           node-version: "10"
 
@@ -44,7 +44,7 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install NodeJS
-        uses: actions/setup-node@v1
+        uses: actions/setup-node@v2
         with:
           node-version: "10"
 

.yamllint.yml

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

modules/bandage/image/meta.yml

@@ -7,38 +7,38 @@ keywords:
     - 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']
+      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 ]
+      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"
+      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 ]
+      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"
+      type: file
+      description: Bandage image in PNG format
+      pattern: "*.png"
     - svg:
-        type: file
-        description: Bandage image in SVG format
-        pattern: "*.svg"
+      type: file
+      description: Bandage image in SVG format
+      pattern: "*.svg"
     - versions:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
 authors:
     - "@heuermh"

modules/dedup/meta.yml

@@ -54,7 +54,5 @@ output:
       description: Dedup log information
       pattern: "*log"
 
-
-
 authors:
   - "@jfy133"

modules/gatk4/createsequencedictionary/meta.yml

@@ -5,28 +5,28 @@ keywords:
     - fasta
 tools:
     - gatk:
-        description: |
-            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/categories/360002369672s
-        doi: 10.1158/1538-7445.AM2017-3590
-        licence: ['Apache-2.0']
+      description: |
+          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/categories/360002369672s
+      doi: 10.1158/1538-7445.AM2017-3590
+      licence: ['Apache-2.0']
 
 input:
     - fasta:
-        type: file
-        description: Input fasta file
-        pattern: "*.{fasta,fa}"
+      type: file
+      description: Input fasta file
+      pattern: "*.{fasta,fa}"
 output:
     - dict:
-        type: file
-        description: gatk dictionary file
-        pattern: "*.{dict}"
+      type: file
+      description: gatk dictionary file
+      pattern: "*.{dict}"
     - versions:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
 authors:
     - "@maxulysse"

modules/gatk4/mutect2/meta.yml

@@ -1,5 +1,5 @@
 name: gatk4_mutect2
-description:  Call somatic SNVs and indels via local assembly of haplotypes.
+description: Call somatic SNVs and indels via local assembly of haplotypes.
 keywords:
   - gatk4
   - mutect2

modules/gffread/meta.yml

@@ -15,9 +15,9 @@ tools:
 
 input:
   - gff:
-        type: file
-        description: A reference file in either the GFF3, GFF2 or GTF format.
-        pattern: "*.{gff, gtf}"
+      type: file
+      description: A reference file in either the GFF3, GFF2 or GTF format.
+      pattern: "*.{gff, gtf}"
 
 output:
   - gtf:

modules/gunzip/meta.yml

@@ -5,29 +5,29 @@ keywords:
     - compression
 tools:
     - gunzip:
-        description: |
-            gzip is a file format and a software application used for file compression and decompression.
-        documentation: https://www.gnu.org/software/gzip/manual/gzip.html
-        licence: ['GPL-3.0-or-later']
+      description: |
+          gzip is a file format and a software application used for file compression and decompression.
+      documentation: https://www.gnu.org/software/gzip/manual/gzip.html
+      licence: ['GPL-3.0-or-later']
 input:
     - meta:
-        type: map
-        description: |
-          Optional groovy Map containing meta information
-          e.g. [ id:'test', single_end:false ]
+      type: map
+      description: |
+        Optional groovy Map containing meta information
+        e.g. [ id:'test', single_end:false ]
     - archive:
-        type: file
-        description: File to be compressed/uncompressed
-        pattern: "*.*"
+      type: file
+      description: File to be compressed/uncompressed
+      pattern: "*.*"
 output:
     - gunzip:
-        type: file
-        description: Compressed/uncompressed file
-        pattern: "*.*"
+      type: file
+      description: Compressed/uncompressed file
+      pattern: "*.*"
     - versions:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/lissero/meta.yml

@@ -41,4 +41,3 @@ output:
 
 authors:
   - "@rpetit3"
-

modules/macs2/callpeak/meta.yml

@@ -1,10 +1,10 @@
 name: macs2_callpeak
 description: Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments
 keywords:
-    - alignment
-    - atac-seq
-    - chip-seq
-    - peak-calling
+  - alignment
+  - atac-seq
+  - chip-seq
+  - peak-calling
 tools:
   - macs2:
       description: Model Based Analysis for ChIP-Seq data

modules/muscle/meta.yml

@@ -1,15 +1,15 @@
 name: muscle
 description: MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options are provided that give you the choice of optimizing accuracy, speed, or some compromise between the two
 keywords:
-    - msa
-    - multiple sequence alignment
+  - msa
+  - multiple sequence alignment
 tools:
   - muscle:
-      description: MUSCLE is a multiple sequence alignment tool with high accuracy and throughput
-      homepage: https://www.drive5.com/muscle
-      documentation: http://www.drive5.com/muscle/muscle.html#_Toc81224840
-      doi: "https://pubmed.ncbi.nlm.nih.gov/15034147/"
-      licence: ['http://www.drive5.com/muscle/manual/license.html']
+    description: MUSCLE is a multiple sequence alignment tool with high accuracy and throughput
+    homepage: https://www.drive5.com/muscle
+    documentation: http://www.drive5.com/muscle/muscle.html#_Toc81224840
+    doi: "https://pubmed.ncbi.nlm.nih.gov/15034147/"
+    licence: ['http://www.drive5.com/muscle/manual/license.html']
 input:
   - fasta:
       type: file

modules/seacr/callpeak/meta.yml

@@ -1,4 +1,3 @@
-
 name: seacr_callpeak
 description: Call peaks using SEACR on sequenced reads in bedgraph format
 keywords:
@@ -11,44 +10,44 @@ keywords:
     - seacr
 tools:
     - seacr:
-        description: |
-            SEACR is intended to call peaks and enriched regions from sparse CUT&RUN
-            or chromatin profiling data in which background is dominated by "zeroes"
-            (i.e. regions with no read coverage).
-        homepage: https://github.com/FredHutch/SEACR
-        documentation: https://github.com/FredHutch/SEACR
-        licence: ['GPL-2.0-only']
+      description: |
+          SEACR is intended to call peaks and enriched regions from sparse CUT&RUN
+          or chromatin profiling data in which background is dominated by "zeroes"
+          (i.e. regions with no read coverage).
+      homepage: https://github.com/FredHutch/SEACR
+      documentation: https://github.com/FredHutch/SEACR
+      licence: ['GPL-2.0-only']
 input:
     - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
+      type: map
+      description: |
+          Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
     - bedgraph:
-        type: file
-        description: |
-            The target bedgraph file from which the peaks will be calculated.
+      type: file
+      description: |
+          The target bedgraph file from which the peaks will be calculated.
     - ctrlbedgraph:
-        type: file
-        description: |
-            Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.
+      type: file
+      description: |
+          Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.
     - threshold:
-        type: value
-        description: |
-            Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph
+      type: value
+      description: |
+          Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph
 output:
     - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
+      type: map
+      description: |
+          Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
     - bed:
-        type: file
-        description: Bed file containing the calculated peaks.
-        pattern: "*.bed"
+      type: file
+      description: Bed file containing the calculated peaks.
+      pattern: "*.bed"
     - versions:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
 authors:
     - "@chris-cheshire"

modules/seqkit/split2/meta.yml

@@ -5,35 +5,35 @@ keywords:
     - fastq
 tools:
     - seqkit:
-        description: |
-            Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
-        homepage: https://github.com/shenwei356/seqkit
-        documentation: https://bioinf.shenwei.me/seqkit/
-        doi: 10.1371/journal.pone.0163962
-        licence: ['MIT']
+      description: |
+          Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
+      homepage: https://github.com/shenwei356/seqkit
+      documentation: https://bioinf.shenwei.me/seqkit/
+      doi: 10.1371/journal.pone.0163962
+      licence: ['MIT']
 input:
     - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+      type: map
+      description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
     - reads:
-        type: file
-        description: FastQ files
-        pattern: "*.{fq.gz/fastq.gz}"
+      type: file
+      description: FastQ files
+      pattern: "*.{fq.gz/fastq.gz}"
 output:
     - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+      type: map
+      description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
     - reads:
-        type: file
-        description: Split fastq files
-        pattern: "*.{fq.gz/fastq.gz}"
+      type: file
+      description: Split fastq files
+      pattern: "*.{fq.gz/fastq.gz}"
     - versions:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
 authors:
     - "@FriederikeHanssen"