add modules for bwa-mem2

tools/bwa-mem2/index/main.nf

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+process bwa-mem2_index {
+    tag {fasta}
+
+    container 'quay.io/biocontainers/bwa-mem2:2.0--he513fc3_0'
+
+    input:
+        path(fasta)
+
+    output:
+        path("${fasta}.*")
+
+    script:
+    """
+    bwa-mem2 index ${fasta}
+    """
+}

tools/bwa-mem2/index/meta.yml

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+name: bwa-mem2 index
+description: create indexes for BWA from a fasta file
+keywords:
+    - index
+tools:
+    - bwa:
+        description: |
+            Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.
+            It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.
+        homepage: https://github.com/bwa-mem2/bwa-mem2
+        documentation: https://github.com/bwa-mem2/bwa-mem2
+        arxiv: arXiv:1303.3997
+input:
+    -
+        - input:
+            type: file
+            description: Input fasta file
+            pattern: *.{fasta,fa}
+output:
+    -
+        - index:
+            type: file
+            description: bwa indexes file
+            pattern: *.{fasta,fa}.{amb,ann,bwt,pac,sa}
+authors:
+    - @maxulysse

tools/bwa-mem2/index/test/main.nf

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+#!/usr/bin/env nextflow
+nextflow.preview.dsl = 2
+include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
+include '../main.nf' params(params)
+
+// Define input channels
+input = '../../../test-datasets/tools/bwa/index/input/reference.fasta'
+Channel
+  .from(input)
+  .set { ch_input }
+
+// Run the workflow
+workflow {
+    fastqc(ch_input)
+    // .check_output()
+}

tools/bwa-mem2/index/test/nextflow.config

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