From 177bf6946444f27aba6f99e6e0094c97f82e47eb Mon Sep 17 00:00:00 2001
From: Stephen Watts <hello@stephen.ac>
Date: Tue, 19 Mar 2024 18:52:17 +1100
Subject: [PATCH] Use Bioconda/BioContainers for bwa-mem2 module

---
 modules/local/bwa-mem2/mem/Dockerfile      | 19 -------------------
 modules/local/bwa-mem2/mem/environment.yml |  9 +++++++++
 modules/local/bwa-mem2/mem/main.nf         |  6 ++++--
 3 files changed, 13 insertions(+), 21 deletions(-)
 delete mode 100644 modules/local/bwa-mem2/mem/Dockerfile
 create mode 100644 modules/local/bwa-mem2/mem/environment.yml

diff --git a/modules/local/bwa-mem2/mem/Dockerfile b/modules/local/bwa-mem2/mem/Dockerfile
deleted file mode 100644
index ba36b89b..00000000
--- a/modules/local/bwa-mem2/mem/Dockerfile
+++ /dev/null
@@ -1,19 +0,0 @@
-FROM docker.io/mambaorg/micromamba:1.5.6
-
-USER root
-
-RUN \
-    apt-get update && \
-    apt-get install -y procps && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/*
-
-USER mambauser
-
-RUN \
-    micromamba install -y -n base -c bioconda -c conda-forge \
-        'bwa-mem2 ==2.2.1' \
-        'sambamba ==1.0' && \
-    micromamba clean --all --yes
-
-ENV PATH="/opt/conda/bin:/opt/conda/condabin:${PATH}"
diff --git a/modules/local/bwa-mem2/mem/environment.yml b/modules/local/bwa-mem2/mem/environment.yml
new file mode 100644
index 00000000..571dda57
--- /dev/null
+++ b/modules/local/bwa-mem2/mem/environment.yml
@@ -0,0 +1,9 @@
+name: bwa-mem2_mem
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bwa-mem2=2.2.1
+  - bioconda::samtools=1.19.2
+  - bioconda::sambamba=1.0
diff --git a/modules/local/bwa-mem2/mem/main.nf b/modules/local/bwa-mem2/mem/main.nf
index 2ae102b6..961791eb 100644
--- a/modules/local/bwa-mem2/mem/main.nf
+++ b/modules/local/bwa-mem2/mem/main.nf
@@ -2,8 +2,10 @@ process BWAMEM2_ALIGN {
     tag "${meta.id}"
     label 'process_high'
 
-    // TODO(SW): create BioContainers multi-package image when appropriate
-    container 'docker.io/scwatts/bwa-mem2:2.2.1'
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' :
+        'quay.io/biocontainers/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' }"
 
     input:
     tuple val(meta), path(reads_fwd), path(reads_rev)