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nextflow/plugins/nf-wave/README.md

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+# Wave containers plugin for Nextflow
+
+## Summary
+
+The Wave containers plugin provides integration with the Wave container service for dynamic container building, augmentation, and on-demand software provisioning.
+
+## Get started
+
+To use this plugin, add it to your `nextflow.config`:
+
+```groovy
+plugins {
+    id 'nf-wave'
+}
+```
+
+Enable Wave in your configuration:
+
+```groovy
+wave {
+    enabled = true
+}
+```
+
+Wave automatically builds containers from Conda packages or Dockerfiles defined in your processes.
+
+## Examples
+
+### Basic Wave configuration
+
+```groovy
+plugins {
+    id 'nf-wave'
+}
+
+wave {
+    enabled = true
+}
+
+process {
+    conda = 'samtools=1.17'
+}
+```
+
+### Using Wave with Conda packages
+
+```groovy
+wave {
+    enabled = true
+}
+
+process ALIGN {
+    conda 'bioconda::bwa=0.7.17 bioconda::samtools=1.17'
+
+    script:
+    '''
+    bwa mem ref.fa reads.fq | samtools view -bS - > aligned.bam
+    '''
+}
+```
+
+### Wave with Fusion file system
+
+```groovy
+wave {
+    enabled = true
+}
+
+fusion {
+    enabled = true
+}
+
+process.executor = 'awsbatch'
+workDir = 's3://my-bucket/work'
+```
+
+### Container augmentation
+
+```groovy
+wave {
+    enabled = true
+    strategy = 'conda,container'
+}
+
+process TOOL {
+    container 'ubuntu:22.04'
+    conda 'bioconda::samtools=1.17'
+
+    script:
+    '''
+    samtools --version
+    '''
+}
+```
+
+### Using private registries
+
+```groovy
+wave {
+    enabled = true
+}
+
+docker {
+    registry = 'quay.io'
+}
+```
+
+## Resources
+
+- [Wave Documentation](https://docs.seqera.io/wave)
+- [Wave Integration Guide](https://nextflow.io/docs/latest/wave.html)
+
+## License
+
+[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0)