From 41dfaf2a19927a5e3b90711d3e55eac3c5e6f47d Mon Sep 17 00:00:00 2001 From: drpatelh Date: Mon, 8 Feb 2021 00:44:45 +0000 Subject: [PATCH] Use Nextflow comments --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index dc4b0ebe..54bbf424 100644 --- a/README.md +++ b/README.md @@ -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. ```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) { - 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 { - container "quay.io/biocontainers/bwa:0.7.17--hed695b0_7" ## Docker image + container "quay.io/biocontainers/bwa:0.7.17--hed695b0_7" // Docker image } ```