Fix indents

software/SOFTWARE/TOOL/meta.yml

@@ -4,74 +4,75 @@ name: software_tool
 ## TODO nf-core: Add a description and keywords
 description: Run FastQC on sequenced reads
 keywords:
-  - Quality Control
+    - quality control
-  - QC
+    - qc
-  - Adapters
+    - adapters
+    - fastq
 tools:
-  ## TODO nf-core: Change the name of "software_tool" below
+    ## TODO nf-core: Change the name of "software" below
-  - software_tool:
+    - software:
-      ## TODO nf-core: Add a description and other details for the tool below
+        ## TODO nf-core: Add a description and other details for the software below
-      description: |
+        description: |
-        FastQC gives general quality metrics about your reads.
+            FastQC gives general quality metrics about your reads.
-        It provides information about the quality score distribution
+            It provides information about the quality score distribution
-        across your reads, the per base sequence content (%A/C/G/T).
+            across your reads, the per base sequence content (%A/C/G/T).
-        You get information about adapter contamination and other
+            You get information about adapter contamination and other
-        overrepresented sequences.
+            overrepresented sequences.
-      homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+        homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-      documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
+        documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
 ## TODO nf-core: If you are using any additional "params" in the main.nf script of the module add them below
 params:
-  - outdir:
+    - outdir:
-      type: string
+        type: string
-      description: |
+        description: |
-        The pipeline's output directory. By default, the module will
+            The pipeline's output directory. By default, the module will
-        output files into `$params.outdir/<SOFTWARE>`
+            output files into `$params.outdir/<SOFTWARE>`
-  - publish_dir_mode:
+    - publish_dir_mode:
-      type: string
+        type: string
-      description: |
+        description: |
-        Value for the Nextflow `publishDir` mode parameter.
+            Value for the Nextflow `publishDir` mode parameter.
-        Available: symlink, rellink, link, copy, copyNoFollow, move.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
-  - conda:
+    - conda:
-      type: boolean
+        type: boolean
-      description: |
+        description: |
-        Run the module with Conda using the software specified
+            Run the module with Conda using the software specified
-        via the `conda` directive
+            via the `conda` directive
 ## TODO nf-core: Add a description of all of the variables used as input
 input:
-  - meta:
+    - meta:
-      type: map
+        type: map
-      description: |
+        description: |
-        Groovy Map containing sample information
+            Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test', single_end:false ]
-  - reads:
+    - reads:
-      type: file
+        type: file
-      description: |
+        description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+            List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
+            respectively.
-  - options:
+    - options:
-      type: map
+        type: map
-      description: |
+        description: |
-        Groovy Map containing module options for passing command-line arguments and
+            Groovy Map containing module options for passing command-line arguments and
-        output file paths.
+            output file paths.
 ## TODO nf-core: Add a description of all of the variables used as output
 output:
-  - meta:
+    - meta:
-      type: map
+        type: map
-      description: |
+        description: |
-        Groovy Map containing sample information
+            Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test', single_end:false ]
-  - html:
+    - html:
-      type: file
+        type: file
-      description: FastQC report
+        description: FastQC report
-      pattern: "*_fastqc.html"
+        pattern: "*_{fastqc.html}"
-  - zip:
+    - zip:
-      type: file
+        type: file
-      description: FastQC report archive
+        description: FastQC report archive
-      pattern: "*_fastqc.zip"
+        pattern: "*_{fastqc.zip}"
-  - version:
+    - version:
-      type: file
+        type: file
-      description: File containing software version
+        description: File containing software version
-      pattern: "*.version.txt"
+        pattern: "*.{version.txt}"
 ## TODO nf-core: Add your GitHub username below
 authors:
-  - "@your_github_username"
+    - "@your_github_username"

software/SOFTWARE/TOOL/test/nextflow.config

@@ -1,20 +1,20 @@
 
 params {
-  outdir = "output/"
+    outdir = "output/"
-  publish_dir_mode = "copy"
+    publish_dir_mode = "copy"
-  conda = false
+    conda = false
 }
 
 profiles {
-  conda  {
+    conda  {
-    params.conda = true
+        params.conda = true
-  }
+    }
-  docker {
+    docker {
-    docker.enabled = true
+        docker.enabled = true
-    docker.runOptions = '-u \$(id -u):\$(id -g)'
+        docker.runOptions = '-u \$(id -u):\$(id -g)'
-  }
+    }
-  singularity {
+    singularity {
-    singularity.enabled = true
+        singularity.enabled = true
-    singularity.autoMounts = true
+        singularity.autoMounts = true
-  }
+    }
 }