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drpatelh 2021-02-08 00:44:45 +00:00
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@ -205,11 +205,11 @@ using a combination of `bwa` and `samtools` to output a BAM file instead of a SA
- Software requirements SHOULD be declared within the module file using the Nextflow `container` directive. For single-tool BioContainers, the simplest method to obtain the Docker container path is to replace `bwa` with your tool name in this [Quay.io link](https://quay.io/repository/biocontainers/bwa?tab=tags). You will see a list of tags sorted by the most recent. You can then use exactly the same name (e.g. `bwa`) version (e.g. `0.7.17`) and tag (e.g. `hed695b0_7`) to add all of the Conda, Docker and Singularity definitions in the module. - Software requirements SHOULD be declared within the module file using the Nextflow `container` directive. For single-tool BioContainers, the simplest method to obtain the Docker container path is to replace `bwa` with your tool name in this [Quay.io link](https://quay.io/repository/biocontainers/bwa?tab=tags). You will see a list of tags sorted by the most recent. You can then use exactly the same name (e.g. `bwa`) version (e.g. `0.7.17`) and tag (e.g. `hed695b0_7`) to add all of the Conda, Docker and Singularity definitions in the module.
```nextflow ```nextflow
conda (params.enable_conda ? "bioconda::bwa=0.7.17=hed695b0_7" : null) ## Conda package conda (params.enable_conda ? "bioconda::bwa=0.7.17=hed695b0_7" : null) // Conda package
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7" ## Singularity image container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7" // Singularity image
} else { } else {
container "quay.io/biocontainers/bwa:0.7.17--hed695b0_7" ## Docker image container "quay.io/biocontainers/bwa:0.7.17--hed695b0_7" // Docker image
} }
``` ```