Update bwa index docs

software/bwa/index/meta.yml

@@ -1,25 +1,52 @@
-name: bwa index
+name: bwa_index
-description: create indexes for BWA from a fasta file
+description: Create BWA index for reference genome
 keywords:
   - index
+  - fasta
+  - genome
 tools:
   - bwa:
       description: |
-            BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
+        BWA is a software package for mapping DNA sequences against
+        a large reference genome, such as the human genome.
       homepage: http://bio-bwa.sourceforge.net/
       documentation: http://www.htslib.org/doc/samtools.html
       arxiv: arXiv:1303.3997
+params:
+  - outdir:
+      type: string
+      description: |
+        The pipeline's output directory. By default, the module will
+        output files into `$params.outdir/<SOFTWARE>`
+  - publish_dir_mode:
+      type: string
+      description: |
+        Value for the Nextflow `publishDir` mode parameter.
+        Available: symlink, rellink, link, copy, copyNoFollow, move.
+  - conda:
+      type: boolean
+      description: |
+        Run the module with Conda using the software specified
+        via the `conda` directive
 input:
-    -
+  - fasta:
-        - input:
       type: file
-            description: Input fasta file
+      description: |
-            pattern: "*.{fasta,fa}"
+        Input genome fasta file
+  - options:
+      type: map
+      description: |
+        Groovy Map containing module options for passing command-line arguments and
+        output file paths.
 output:
-    -
   - index:
       type: file
-            description: bwa indexes file
+      description: BWA genome index files
-            pattern: "*.{fasta,fa}.{amb,ann,bwt,pac,sa}"
+      pattern: "*.{fasta}.{amb,ann,bwt,pac,sa}"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.version.txt"
 authors:
+  - "@drpatelh"
   - "@maxulysse"