Copy across test data and docs for bwa mem

software/bwa/mem/meta.yml

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+name: bwa mem
+description: Performs fastq alignment to a fasta reference using the burrows-wheeler aligner
+keywords:
+    - mem
+    - bwa
+    - alignment
+tools:
+    - bwa:
+        description: |
+            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
+input:
+    -
+        - id:
+            type: val
+            description: read/read pair id
+        - reads:
+            type: file
+            description: Input fastq file
+            pattern: "*.{fastq,fq}"
+        - index:
+            type: file
+            description: bwa indexes file
+            pattern: "*.{amb,ann,bwt,pac,sa}"
+        - prefix:
+            type: val
+            description: bwa index prefix, equivalent to index file names without extensions. Usually the reference genome file name unless otherwise specified.
+output:
+    -
+        - bam:
+            type: file
+            description: Output bam file
+            pattern: "*.bam"
+        - bamindex:
+            type: file
+            description: Output bam index file
+            pattern: "*.bai"
+
+authors:
+    - "@jeremy1805"

software/bwa/mem/test/main.nf

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+#!/usr/bin/env nextflow
+nextflow.preview.dsl = 2
+include '../../../../tests/functions/check_process_outputs.nf' params(params)
+include '../main.nf' params(params)
+
+reads = '../../../../test-datasets/tools/bwa/mem/reads/*_R{1,2}_001.fastq.gz'
+index = '../../../../test-datasets/tools/bwa/mem/index/H3N2.{amb,ann,bwt,pac,sa}'
+prefix = 'H3N2'
+
+workflow {
+  read_input=Channel.fromFilePairs(reads)
+  bwa_mem(read_input,file(index),prefix)
+}

software/bwa/mem/test/nextflow.config

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+docker.enabled = true
+params.outdir = './results'